Coral Bleaching on Inshore Reefs near Cairns

The 2016 coral bleaching on the Great Barrier Reef has been received a lot of attention but I am not sure that anyone has documented what has happened on the inshore reefs and coastal fringing reefs.  In this post, I present my observations of Yule Reef before and after the summer of 2015-6. Yule Reef is part of the coastal reef complex just south of Port Douglas.  At low tide the 4.5 km long reef can be accessed by foot from the Captain Cook Highway which makes it the most easily accessible coral reef near Cairns.  The only equipment needed to get to the reef is a pair of shoes to protect from stonefish.

Yule Reef, with Captain Cook Highway visible at Yule Point in lower right (Photo 1996, Beach Protection Authority)

Inshore reefs are not as pretty as off-shore reef but like any place with high biodiversity they are interesting.  Yule Reef supports a variety of large marine animals, particularly green and hawksbill turtles. Inshore reefs also function like a giant water filter that can make murky coastal waters clear. On the outgoing tide when clear water from the reef flat spills through channels in the edges of the reef, I used to snorkel between the coral platforms as the enclosed shallow waters were also safe from tiger sharks.

One of the channels between old coral platforms (July 2012) - click to zoom in

Closer to the reef edge there is respectable coral in the channels (June 2009)

Another coral view in a channel at Pretty Beach (about 50 m off the beach and 3 km further south)

I was slow to discover inshore reefs as even back in the 1980’s common people were saying that most of the inshore reefs were dead.  I now know that there has been approximately 1 m of tectonic uplift in the previous 6000 years and that this may have thrust the tops of reef up above the level of reef growth.  The channels in the reef and the outer edge are where most of the life is.  Corals on inshore reefs are also predominantly grays and brown rather than the riot of pastel colours seen on the outer barrier and this may have lead to the idea that the reefs were dead.

Dense soft corals at the head of the shallow channel where people enter the reef from the sand flats (July 2009)

Many inshore reefs have parallel coral platforms tens of metres long and a few metres wide that point seaward like widely spaced piano keys (the streaks in the aerial photo). The tops of the platforms are brown and sometimes muddy but have their own life forms. Coral cover on the sides of the channels was high, although only a few coral species were present. At low tide, rays, turtles and large fish such as metre long Australian salmon are often present in the channels presenting an opportunity to observe these animals.

Coral platforms that appear as a dark fringe near the seaward edge of the reef on the aerial photo.

Describing what the reef was like before the 1998 coral bleaching is very hard.  When I first visited these reefs there were no affordable underwater cameras and GPS did not exist so making a good record was out of reach.  Even aerial photography was hard to come by.  To remember where places were, I would try to line up coastal features with mountains, a method that was very approximate at best.  Added complications included persistent rough conditions  that would muddy the water and make navigating around reefs difficult and the presence a wide range of potentially lethal animals including tiger sharks, crocodiles and box jellyfish.  Seasonal growth of Sargassum weed can also cover much of the reef with floating towers of brown seaweed over 2 m tall.

Now I use a GPS (Garmin 64s) and an underwater camera and on my last day trip to the area, captured almost 700 photos.  Geotagging software is used to geotag the photos with the GPS trail, which results in a better than 3 m geographic precision.  In-camera GPS units are far inferior to hand held GPS units so I overwrite any coordinates recorded by the camera.  Now, I have a record that rivals the environmental monitoring undertaken by some scientific organisations.

Starting with my old memories from the time before the first coral bleaching in 1998, the reef edge near the mouth of the Mowbray River was a slightly threatening place.  Swells would swash between exposed dark brown living heads of coral that rose up approximately a metre from the bottom and stood more than half a metre exposed between waves.  These coral heads, which were shaped like tiny mountain peaks formed an irregular row with roughly 10 m spacings.  With care I could navigate around them with my 12 foot boat and motor.  The heads of living coral may in part be maintained by the splash of waves allowing the coral to grow taller than water levels usually permit.  I wonder if these tall raised coral colonies are still a feature of today’s reef.

A coral head on Little Reef, which is near Yule Reef (June 2009)

Wentworth Reef which is further offshore was a complex of metre high coral ridges covered with low brown seaweed and separated by sinuous sandy channels.  Where the edge of the reef dipped away to the sea floor which was too deep to see given the water clarity, there was a diverse continuous coral cover on the slope.  Large fish were virtually absent and I put this down the accessibility of the reef leading to overfishing.  Coral colonies were frequent and were attended by schools of small reef fish, mostly of the yellow and grey varieties.  Inshore reefs never were as exciting as the outer reef and to be fair, I did not want to swim in the low visibility waters on the reef edges where the best corals were.

Typical underwater view on Wentworth Reef (August 2013)

Heading back to the Mowbray River from Wentworth Reef, I found a slightly deeper reef just out from the main part of Alexandra Reef.  Snorkelling over this reef revealed an almost level surface of living massive coral that was so extensive that dragging a dinghy behind me, I did not have the energy to reach the other side.  In all that distance, probably more than 150 m, I did not observe a single gap in the coral cover.  It would not have been possible to slip a razor blade between the living coral colonies.  At the time, it was considered that a healthy reef would have 50% coral cover and 50% coralline algae cover and as I swam across the reef, I was thinking about how this reef absolutely defied that pattern.  Within the flat mid-brown surface at metre spacings were fist sized holes which were the last vestiges of gaps between colonies.  These gaps provide the only refuges for the small fish that were swimming around above the coral surface.  The reef was completely devoid of larger fish and had no brown macro algae at all.  I don’t know if this reef ever becomes exposed at low tide, but if it did it would have been a struggle for fish to survive on the reef during these periods.

A tiny patch of continuous coral cover showing how there is no space between colonies (July 2012)

I do not know if this reef survived the first coral bleaching in 1998.  It was boring by coral reef standards but from today’s perspective is was a living miracle.  It was a massive seamless monoculture of coral that was only limited by the depth of the available water.  A smaller example of the same type of reef was also present on a small south-facing bay at the far eastern end of Dunk Island (near mangroves).

I have looked for mono-culture brown reef a few times since the 1998 coral bleaching but finding even large reefs that are close to shore can be difficult.  On a day with a mirror-like surface I once failed to find a reef that was less than 1000 m from shore, even though I briefly saw the reef under my boat, the reflective surface defeated my attempts to relocate the reef and the next day, I bought my first GPS out of frustration.  When I searched Alexandra reef for the live coral surface, I found a thick forest of Sargassum which was over 2 m tall.  There was almost no live coral below the sargassum, just an irregular dead coral surface covered with a film of mud.  Very small massive corals were here and there and I put the survival of these corals down to being on vertical surfaces which resist the settlement of sediment.  Now with aerial photography, I have located a small, slightly deeper reef just the east of Alexandra Reef, I need to check that reef as it may be the reef with the living coral surface I once observed.

Sargassum dominates the shallows between the coral platforms near the reef edge and the green seagrass beds on the landward margin of the reef

Tall growths of Sargassum are a seasonal feature of inshore coral reefs and often form a single line close to the transition point from shallow to deeper water.  I cannot say whether the massive growths that now blanket inshore reefs during summer used to be present before the first coral bleaching to the extent they are now.  I also cannot say whether Sargassum competes with coral or protects it.  In deeper water with better water flow, Sargassum may shade the coral and help protect it from bleaching.  In other locations, I suspect that Sargassum alters the environment in ways that are not favourable for coral.  Some research is needed.

Sargassum laying down in a shallow lagoon at low tide (April 2016)

Did this coral survive due to its wig of Sargassum?

Turtles were sometimes abundant and one day I counted 30 turtles on a 4 km section of reef front.  When turtles are surprised by an object shaped like a shark, they present their back to the shark’s mouth as a turtle's back is its shield.  To angle themselves in this way, they actually have to swim up into the path of the moving object.  In this case, the object was my competition surf ski and I had the unusual experience of turtles sometimes rising from the bottom and deliberately colliding with the front of my craft.  With one turtle, I paddled backwards a few metres, changed direction and set off again to miss the turtle by a few metres only to have the turtle swim into my craft a second time.  Other large wildlife includes dugong, which are almost impossible to sneak up on and you only know they are close when you see metre wide patches of smooth water forming on the surface that indicate a dugong has swum below.  Large predatory fish such as Australian salmon and sharks swim through the shallow waters and stingrays of many species were usually present in large numbers.  I actually stopped swimming in the shallower sandy channels due to the numbers of stingrays in them and this was long before the Irwin tragedy.

After Cyclone Yasi destroy feeding grounds, many exhausted Green Turtles would beach when the tide retreated (July 2012)

By 2012 most of the reef appeared to have recovered from the 1998 bleaching.  The only element that I have not seen again is the massive coral surface and that is possibly due to navigation issues. Some off-shore reefs that were stunning were laid waste by the 1998 bleaching to the point of being unrecognisable so to see that a reef had recovered was really encouraging.

Well before the event, the 2016 coral bleaching was predicted.  Satellites had identified a vast pool of hot water in the eastern pacific ocean and from past experience, it was known that this pool of water would stream across the pacific to affect the Great Barrier Reef.  The 2015-6 wet season was poor and the skies often crystal clear.  On kayaking my wet hands would be cooled by the breeze but when they dipped into the water, the water was as hot as bath and beyond anything I had experienced.  I heard from others that Yule Reef had gone white so I missed the onset of the event and perhaps have only captured the tail end.

On walking out onto the reef flat, the most obvious change were large patches of white coral.  White coral is dying coral which will either die or if conditions suddenly change for the better, recover.

One of the first corals I saw was completely bleached with more exposed parts already dead

In April 2016, Yule Reef was dominated by patches of stark white in a brown Sargassum matrix

The stark white corals are eye-catching however a second view shows than some corals were not bleached

The area shown above was in or near a shallow lagoon behind the coral platforms of the main reef.  Just to the north is a strip of fringing reef where I discovered that fewer people walk and the coral was in great condition (seen on left of aerial photo).  The entire reef flat was covered with a gray turf of living coral.

Living coral grew like a lawn up to the upper limit of growth (July 2012)

A close up of the coral lawn showing two species of branching coral

On revisiting the reef in April 2016, at first sight the reef looked the same. However most of the larger tracts of coral on the reef flat are completely dead.  Some smaller patches of coral in this area still struggling to survive.

The coral is still standing but is dead

A close-up view shows brown slime rather than star shaped coral polyps

Corals in areas with better water flow survived at a least in part

Massive corals (species that grow like boulders) are also present in lower densities and some appear to be fine but others have taken on strange colours.  For massive corals, it seems preferable to be exposed to air, rather than be in the hot waters of the reef shallows.  In the shallows, may corals are not pure white but a florescent light green or yellow.  There were no simple patterns to the bleaching and unaffected corals were scattered through devastated areas.

Stressed massive corals were an abnormal pink colour

Same species of coral bleached to a florescent light green shade

It is clear that huge damage has been done to Yule Reef with coral mortality above 50%.  Inshore reefs regularly take a beating from cyclones and floods so have great powers of recovery, however if the frequency of events increases, there will not be enough time to recover.  There may also be a breakdown of essential processes such as the processes that provide clean hard surfaces for coral larvae to settle on.  To some extent, the process that create good conditions for coral are provided by the coral reef itself.  So Yule Reef survives for now, but it is a diminished place and is on the edge of survival.

Hidden Fauna of Floating Mangrove Litter

For almost every type of floating mangrove debris, there is a marine creature that mimics it.  This post covers some of the mangrove litter mimics in the marina at Cairns in tropical Australia.  There are fish that mimic mangrove leaves, strands of seagrass and flakes of bark.  Surprisingly, not much seems to have been written about fish that mimic floating leaf litter. 

Floating mangrove litter can be surprisingly busy with many creatures being present around the same patch of litter.   The best places are where floating litter is spread out in thin lines or small patches.  Bigger patches have fewer creatures.  Perhaps they have been eaten by predators that pick over the larger patches.  Whilst mimics depend on looking like non-food objects, they would also benefit for being spread out thinly over a large area.

Leatherjacket mimicing tree bark (click to zoom in)

Pipefish that mimics floating seagrass leaves (the coarser Zostera leaves)

Mimicry is usually defined as a potential prey species closely resembling another animal species that is unpalatable or dangerous.  The term camouflage is used when an animal blends in with its environment.  However the fish shown in this post are closely resembling the appearance and behavior of discrete floating objects so I would considered the fish as mimics rather than camouflaged species. Many fish actually lie on their sides at the surface when threatened to better imitate floating litter.  This active imitation of the orientation and motion of floating objects goes beyond camouflage.

Unidentified green fish in the head down position beside a mangrove leaf

Same fish pretending to be a leaf when a herring approaches

The surface waters are also home to a number of specialised hunters that do not make use of mangrove litter.  All of these fish have excellent vision and can see predatory birds through the water surface and they relay mainly on speed rather than blending in.  Garfish and Archer fish are abundant. These large fish prey on small fish in the surface waters.

Sevenspot Archerfish checking out a black mangrove seed that looks like a baby squid

Longtoms patrol the open waters

Tiny fish seem to find refuge in a thin layer of water held by upside down leaves against the surface.

Unidentified fish hiding on top of a mangrove leaf

Small grunters are audacious hunters that attack tiny juvenile fish even when they are hiding on top of leaves.  Grunters can zip around at such speed that nothing could escape from them and very little could catch them.  Whereas most creatures of the floating litter move as little as possible, grunters are constantly moving, stopping briefly whilst they carefully observe their surrounds for potential prey.  The largescale grunter which were hunting in the mangrove litter often passed very close to mangrove litter mimics and either did not see them or avoided them on the basis that they were too big or too heavily armoured (scats and pipefish).

A grunter trying get to the garfish on the leaf

Same 50 mm long grunter hiding behind a mangrove flower

Tiny squid are abundant in the floating litter and larger squid often patrol just below.  Squid are predators and aggressively attack fish and even tiny squid would be a threat to juvenile fish.

Baby squid preparing to attack 

A bizarre creature that looked like a small section of tree branch covered by rough bark was flapping its way along like a hatchling sea turtle.  It was just an Estuarine Stonefish, but you don’t expect to see those feeding on the surface.  Scientific advice from a scorpion fish researcher is that stonefish do not have swim bladders so how it was managing to float was unclear.  It was however feeding.  In cases like this, a second observation of a different individual behaving in the same way is needed to establish that the behaviour could be normal behaviour for the species and not just an observation of an individual where something is wrong.    

Estuarine stonefish feeding on the surface

Mangrove herons also take a professional interest in the fauna of floating mangrove litter.  

Mangrove heron on floating walkway

Fauna in the Swash Zone of a Tropical Beach

Swash is the foaming surge of water that runs up the face of a beach after a wave breaks.  This narrow habitat has its own distinct fauna, a fauna which is well documented in cold countries that have lots of beaches but is almost undocumented in the tropics where people tend to focus on corals and mangroves. 

Low tide terrace of Yorkeys Knob Beach is prime swash fauna habitat, even for mole crabs

The swash zone is full of life and has many species that are not found on sand flats that are exposed at low tide.  On a remote beach, I once grabbed a handful of sand and counted 17 pipis of varying sizes in that single handful.  Here is a video that shows migrating pipi, filter feeding worms, a common moon crab and pied oystercatcher feeding on pipi.


Each beach has its own wave and sand characteristics and the fauna present vary greatly.  In North Queensland, there is a spectrum of beaches from steep beaches with coarse sand and almost flat beaches with fine sand.  The best beaches for fauna are the beaches between the two extremes.  Most of the swash fauna migrate up and down the beach with the tides, probably to escape predation.  When a beach is very flat, the distances between high and low tide swash zones becomes very far and the swash becomes so slow and gentle that it does not liquefy the sand.  Most of the migrating swash fauna also need the sand to be mobilised or liquefied by waves so that they can burrow into it.  Burrowing into hard packed sand is very difficult for many creatures.  At the other end of the spectrum are steep beaches with coarse sand where waves crash down hard on bare sand.  Very little fauna can be found in these beaches.  Beaches that do not have swash such as beaches within river mouths also do not have much fauna.

Swash zone fauna do not like waves that crash down on the beach

Pipi (officially called Cuneate Wedge Shells – Donax cuneatus) are the best know inhabitant of the tropical swash zone.  People dig them up and take them home to fry, spice and eat.  Pipi came to be of interest me when I noticed that they eject themselves from the sand so that waves can carry them up the beach.  On my favourite beach, the slope is steep and the swash moves very quickly so the pipi have to be very decisive about which waves to catch and with regard to timing.  Everything is so fast that it too fast for human vision and I resorted to using high speed video which is how I saw that pipi sometimes jump out of the sand microseconds before or after the arrival of the wave.  Now I have found out that pipi move in a much more relaxed fashion on shallow sloping beaches and can easily be observed with the naked eye.  The gentler swash on these beaches do not always move the pipi far enough and the pipi somehow know!  They just lie there on the surface waiting for another wave.  Sometimes up to 3 waves are needed to move the pipi up the beach and make it happy.  Then it wiggles its foot vigorously into the sand and pulls its shell down before the wave retreats and the sand goes hard.  Very occasionally, a pipi will be taken too far up the beach and they just wait for a big wave to take them back down again. 

Pipi (Cuneate Wedge Shell, with foot and siphons exposed

Pipi can use their siphons like arms to push into the sand and hold themselves against the retreating swash.  They also use their foot to dig into the sand like an anchor, however I think as swash usually undermines the sand out from beneath my feet, that the foot of the pipi mainly perform a hydrodynamic role and prevent the sand from being undermined from under the pipi. 
Much rarer than pipi are mole crabs.  I have only ever caught one.  They are neither common or easy to find.  Mole crabs filter feed with their antennae.

A mole crab - Albunea-symmysta

The entire undersurface of Albunea is dedicated to digging implements

Feeding Albunea poke their antennae into the retreating swash

On beaches with fine sand, tiny filter feeding worms are the most common creatures and they cover the entire surface of the beach.  These worms have burrows where they can wait between tides rather than migrating.  Finding out what the worms are called is a mission as almost nobody writes about these creatures even though they are so common that they must be ecologically important.  I think that they may be a type of palp worm (Spionidae).

Head and palps of filter feeding worms, click to enlarge as they are hard to see

The filter feeding worms are quite small

However the spionid? worms cover the beach

Matuta victor crabs patrol within the surging swash.  There seems to be a Matuta crab every few metres, which is a similar density to ghost crabs which scavenge the beach at low tide.  Matuta are reported to eat bivalves and worms so are probably the primary predators of the pipi and spionid worms. 

Common Moon Crab - Matuta victor

Fish are also present within the swash.  Fourline Striped Grunter, Pelates quadrilineatus zoom around in the swash.  A few times I saw a small sole allowing itself to be beached as the swash retreated.  It could see me coming and always escaped.

When the tide retreats, the swash zone also provides food for ghost crabs and pied oystercatcher.

Pied Oystercatcher feeding on Wedge Shells

Baby horn-eyed ghost crab

There are probably several creatures present within the swash zone waiting to be discovered. With waves constantly moving everything around, it is a very difficult place to study.

Shrimp dug up in swash zone

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The Secret Power of Ordinary Coastal Processes

For a long time geomorphologists (people who study how landscapes evolve) thought that is was mainly day to day coastal processes that shaped our coastline.  Then came a realisation that many coastal features were in fact created by major events from super cyclones to tsunamis.  Major events then became the main focus of study.  But there seems to be another agent of change that possibly has as much effect as major events and this is synergies of ordinary events.  In more than twenty years of observations of the Cairns Northern Beaches, these synergies have caused more beach erosion than several major cyclones. In this post and a future post, I will describe two synergies that can move vast amounts of sand in periods of hours.

One of most dynamic sections of coastline near Cairns is Barr Creek, which lies between Machans Beach and Holloways Beach.  This tiny little creek is only 1.2 km long, yet it can turn ordinary tides into dramatic events.  Barr Creek is unlike all of the other creeks in the region as it is an ancient abandoned mouth of the Barron River.  The other creeks have catchments on side the mountain ranges and their channels are maintained by flooding rains draining back to the sea.  Barr Creek barely has any catchment at all, just fringing mangrove swamps.  In theory, when turbid seawater fills into the Barr Creek at high tide, sediment should settle out of the still water and rapidly fill the creek in.  This is exactly what happened in the nearby Blind Barron, a mouth that was abandoned approximately 70 years ago.  Yet Barr Creek maintains itself.

The mouth of Barr Creek migrates from side to side

Most of Barr Creek can be seen from the beach

Barr Creek 1 km upstream is almost too small to turn a small boat

Barr Creek's secret is that it has flood-like outgoing tides.  No other creek in the region has these.  I suspect that on highest astronomical tides (~3.3 m), seawater expands over an almost flat ground surface in areas with mangroves and salt pan.  As tides get higher, the area that is flooded increases exponentially and the volume of water in the Barr Creek estuary would be much greater for an extreme high tide than a normal high tide.  When the tide turns, all of that extra water has to squeeze out of a creek mouth that is always being narrowed as longshore drift fills the mouth with sand at a rapid rate.  Longshore drift occurs when trade wind driven waves strike the beach at an angle and their swash pushes sand along the beach.  On the outgoing tide, waters flood out through the narrowed mouth at high speed creating standing waves that can be more than a metre high.  Ocean swells also force their way up into the outgoing flood and momentarily transform standing waves into raging peaks of water as they pass.  When conditions were like this we used to drop everything and go white water rafting (the video does not show a full power day).  After the flood has surged more than one hundred metres out to sea it plunges through a rolling wave than marks the end of the flood and the start of the sea.

Underneath the surface the outgoing flood is a turbulent maelstrom.  The sandy bottom is not smooth but a complex pattern of mega ripples and swirling vortexes that vacuum sand of the bottom and inject it into the flowing water.  A single tide can transport enough sand to create an alluvial fan that extends 100 m into the sea and which would require more than 2500 tonnes of sand by rough calculation.  A continually rolling wave is located at the seaward edge of the alluvial fan.  Inshore waters are shallow so the alluvial fan ends with a steep drop of only half a metre.

Strong longshore drift removes the alluvial fan within a few days to weeks.  The same longshore drift brings new sand to the creek mouth where it is sucked up the creek to form an alluvial fan that faces upstream.  Sand accumulated in the creek mouth in this way provides material for forming a fan in the sea when the tide runs out.

Aerial view showing both alluvial fans.  The fan in the sea is 85 m long and is mainly from one tide.

It is amazing how big the alluvial fans can get.  At the front-left are a few mega-ripples

Beaches often seem to be static places, adjusting only slowly to the balance between accretion and erosion, however the truth is that every wave moves more sand than a good man can shovel in a minute.  Usually the amount of sand added and removed is in balance.  It is only in special places where sand movements are not balanced that true level of movement is revealed.

Kids love the high banks where the creek cuts into the beach

Getting rolled along by the incoming tide is fun too!

There is a funny side to the Barr Creek tidal movements.  Years ago Holloways Beach had a pub and Machans did not.  So people would come across the creek at low tide then go home in the dark.  At night you can’t see power of the water or its depth.  Many people have been swept away attempting to cross the creek.  Lucky they could all swim.  The incoming tide is pretty nasty too and some people got swept up the creek into the mangroves and you can imagine the fun: drunk in the dark and staggering through the mangroves.

On a particularly violent day when outgoing tide was reinforced with a freshwater flood, I was out there having fun when a rescue helicopter came out and started circling around me.  I was trying to surf the standing waves on a competition surf ski which can be paddled to about 15 km/h.  But the water was much faster and I would paddle upstream like mad whilst getting sucked backward through the flood until I caught a standing wave and hopefully surfed.  Of course you can’t see what is coming when you are going backwards which makes it very exciting and it is almost impossible to go through the roller backwards without coming off.  Beyond the roller is flat calm sea so you just get back onto the surf ski, paddle to the beach and go again.  Of course the rescue helicopter shows up just at the point of wipe out and thinks I am in trouble and started preparing to rescue me, which was embarrassing.

Barr Creek mouth widened to 60 m after a cyclone when Barron River water flowed through fields into Barr Creek 

In this post I have talked about how a synergy of ordinary events can create very powerful forces.  In a future post, I will show the damage this process can do when it combines with other ordinary events to create an extra-ordinary synergy.

For more information on coastal processes, see the subject index