No, the fish don’t all leave en masse! We’ve all seen those distributing social media clips of people cast-netting for kob and garrick as they attempt to exit recently opened South African estuaries mouths. But what really happens to the fish that have been trapped in those closed systems?

“Some 70% of South African estuaries are classified as Temporarily Open/Closed Estuaries. We call them ‘TOCEs,” says Professor Paul Cowley, the Principal Aquatic Biologist at South African Institute for Aquatic Biodiversity (SAIAB). “They are the dominant estuary type among our 250-odd functional South African estuaries and obviously serve a very important nursery function and home to fishes.” Prof Cowley lives in the Eastern Cape and has two TOCEs on his doorstep. Over the past 30 years he’s made some interesting observations when it comes to closed systems breaching naturally.

River mouth up on the East Coast of South Africa
Dropping tide on an open estuary way up the East Coast

I’m based in the Garden Route with various TOCE systems close by (the likes of Swartvlei, Klein Brak and Great Brak, among others) which are periodically breached artificially by mechanical methods.

Prof Cowley believes that the two types of breaching events influence fish behaviour rather differently (as one might expect from a natural vs a human engineered event), but that some of the main principles apply to both.

garrick on fly
Vivid colouration on a species for the who our estuaries are crucial – the juvenile leerfish (garrick) – from a closed Southern Cape system a few seasons back. (c) LeRoy Botha


During the closed mouth phase, the water level fluctuates depending on the amount of freshwater input (from rain in the catchment) or seawater penetration during extreme rough sea events. Here pulses of big waves rush over the sandbar in the mouth region and supplement the estuary with seawater. These are called ‘over-wash events.’  During times of severe drought the mouth can remain closed for several years and if we don’t have rain the water level can drop due to evaporation. During these times the estuary can get extremely salty and even cause ‘fish kills.’

Estuary breached in SA
An over-wash event at an estuary in the Eastern Cape. (c) Paul Cowley


Natural mouth opening events are driven by rainfall. “What typically happens during the closed phased up here (in the Eastern Cape) is that we’d get rain and then the water level rises to a point that it actually exceeds mean sea level. After sustained good rains – usually in excess of 80-100mm – the sheer volume and seaward push of water in the ‘perched’ estuary causes the mouth to breach,” Cowley explains. “The sandbar is naturally and fairly rapidly eroded away when the estuary bursts open…. and it is actually something quite spectacular to watch.”

Natural estuary breach event after big rains
An Eastern Cape estuary breached after big rains. (c) Cowley


“What I have observed is that the fish don’t just rush out immediately. They slowly move downwards and start aggregating in the mouth region. I suspect they are responding to the freshwater push that is coming down. I’ve even observed some fish swimming upstream. Then they realise it’s too fresh and potentially too turbid (if it’s carrying a bit of a silt load), this forces them to move down and, eventually out into the open ocean.”

According to Cowley it can take four or five hours before the fish (in a naturally breached estuary) to start leaving. “It is usually the smaller fish – the stumpies and the mullet – and then after that you will see the larger fish such as kob, garrick, grunter and steenbras moving out of the system,” he says.

Estuary breached
A day after the picture above, sandbar and water gone. (c) Paul Cowley


“When a bulldozer comes and mechanically opens the mouth there hasn’t been that rapid freshwater drive and I suspect you won’t get the same response, well not exactly anyway. I don’t think all or the bulk of the fish will leave because the water might still be quite suitable for them. Unless the water level drops so much that most of the basin is cleared, or the water quality has deteriorated so much over an extended close period. Another response that might force them to go out is when they are sexually mature – you might find that there are grunter and leerfish that have the urge to get back to sea (where they spawn), so they will take the opportunity to leave that system.”

South African estuaries
Klein Brak estuary earlier in 2021 a few days after a mechanical breach. (c) Van Rensburg

What Prof Cowley finds fascinating, is that some leerfish that he tagged in a closed estuary and remained landlocked for four or five years, became sexually mature and when the estuary broke open they headed out to sea. Once at sea they must have sensed the migration of other leerfish on route to KZN. “I think is it absolutely amazing that these fish had never been in the sea, never migrated before and yet they knew exactly where to go. Some of these large leervis were recaptured in KZN (more than 500km away) within two weeks of the mouth opening here in the Eastern Cape.”


  • The water level drops too low
  • The water quality has deteriorated (and/or freshened) too much
  • Certain species have reached sexual maturity

“Possibly not all of these fish have the same urge to go spawn and because the conditions are favourable – there is plenty food available – so they just stay in the system and keep growing.”

Cowley has also seen large mullet aggregating near the mouth during periods of extended mouth closure. “However, during over-wash events (where the sea water gets pushed over the sand bar into the estuary mouth) you can see some of the large mullet are sensing an opportunity to get back to sea. I’ve also seen them run the gauntlet and even get stranded on the sandbar. The same thing was observed with eels – following some rain, they sense that it’s time and they move down and try get out. But with the mouth being closed the only opportunity exists when big over-wash events occur.”

Why then would unusually large fish (such as garrick) still be found in a system like Swartvlei, even after it’s been open for an extended period of time? “They just don’t go out,” Cowley says. “Possibly not all of these fish have the same urge to go spawn and because the conditions are favourable – there is plenty food available – so they just stay in the system and keep growing.”

This doesn’t mean that these fish are spawning in the system. “Well there won’t be survival if spawning is taking place in these closed systems because the eggs would ultimately settle down on the bottom and die if they did spawn,” Cowley has a hunch that if the ovaries start developing in sexually-mature fish in a system such as Swartvlei and they realise that they can’t get to sea to spawn they do not spawn in the estuary, but rather reabsorb those eggs as sort of an energy reserve.


The recruitment (of juvenile fish into the system) is perhaps an even more interesting topic than mature (or nearly mature) fish exiting the system. Recruitment occurs in two ways in TOCE systems: “When the mouth opens naturally – after good rains – there is a fairly deep channel that links the estuary to the sea, which now allows for recruitment. Usually this is in the form of very small larvae (sort of 1 to 1.5cm long) although some fish will recruit at slightly larger sizes, for example kob would recruit at 5 to 6cm,” Cowley says, that the seasonal timing of a mouth opening is obviously crucial and needs to be linked to the spawning season and hence the availability of juveniles in the marine environment.

“Mullet and stumpnose are spawning for eight months of the year, so there are always juvenile recruits available in the surf zone for those animals to enter when a mouth opens,” he says, highlighting why these are the most dominant species found in TOCEs.

What has always interested me is how fish know how to locate the estuary and turn off their offshore routing and head inland.

Cowley and his team illustrated how this works with a lab experiment some years back. “We did a thing called a ‘choice chamber experiment’,” he says. The team setup tanks with water collected from three different environments: One river water, one estuary water and one marine water. The water flowed out of each tank into a large trough.

“We had larval fish in the big trough and observed them automatically orientating toward the river water and the estuarine water, so they knew which water sample represented that of an estuary (i.e. a nursery area) where they want to end up,” Cowley says. “We changed the salinity of all the water treatments up to 35 parts per 1000 using neutral salt from the Dead Sea, so it wasn’t a salinity response, it was a response to an olfactory cue (the smelling of the water). It could also be that they are smelling other members of the same species living in that water and that is what made them head to that zone of the choice chamber. The response to olfactory cues has also been shown quite clearly in salmon recruiting back into rivers as well as eels.”

As is so often the case with the ocean and its many fish species, there is still a vast amount we do not know about why fish behave the what they do when an estuary is breached naturally or otherwise, but for now put it this way – it’s like a Friday night. Some fish of a certain age and certain species see the opening of an estuary as a Matric Rage/Spring Break and Glastonbury all rolled in to one. A chance to get out there, spread their wild oats, go on a months-long bender, wake up in an Ashram in India and then having found themselves, they find themselves again, back in the estuary of their births. Others, prefer to stay on the couch no matter what as long as the temperature is right and there are loads of snacks. Sounds a bit like people.

“But,” Prof Cowley warns as a final word, “these fish don’t breed in the estuary so any harvesting means that the trapped population just gets smaller (like fishing out of a fish bowl).”

“They also haven’t had a chance to breed yet, so putting them back (practicing catch & release only) will ultimately afford each fish a chance to breed (and add his/her genes to the gene pool) when they eventually get back to sea.”


  1. What happen to the saltwater fish when a river floods with freshwater. Gouritsmond went completely fresh for days.

    • Hi Johann, we asked Alan Whitfield the expert who weighed in on our Troubled Waters Estuary article –

      This was his response:

      “During river flooding the freshwater normally flows through the estuary in the upper layer. The bottom layer, particularly in deeper channel areas and holes, can often remain fairly saline and offer some refuge for marine fish. Obviously if the entire estuary, from top to bottom, is completely fresh then marine fish species will temporarily retreat to the marine environment and return to the estuary once tidal conditions resume. Most marine fish species can tolerate low salinities (e.g. 5 g of salt per litre of water), with the seawater standard being 35 g of salt per litre of water.”


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