Southern Estuary Basics

If you haven’t tried estuaries yet – or only dabbled – Kiel recommends them as your next fly challenge.

The river trout season has closed, three and four weights have been put back in their tubes and many of us trout fishos are starting to look at the lakes. And what a lake season it’s proving to be, with plenty of water and cold temperatures to keep the trout full, happy and fat, as Philip Weigall wrote in his June article Lake Transition.

However, being flyfishers, we’re always looking for more. What’s around the next bend? Maybe the fish are cruising the western shore? It’s the hunt and curiosity that drives a lot of us, so why not take on a challenge. It’s a small step, though it feels intimidating. Have a crack at flyfishing estuaries.

There are many great selling points for fishing estuaries. The ocean is close by, birds and sand dunes, waves crashing in the distance. Walking sand flats instead of mud-lined shores. And the perfect setting for fish & chips at the end of the day.

Late winter on an East Gippsland estuary – where would you rather be?


There is an abundance of species to fish to. From flathead to bass, mullet, estuary perch and bream. Garfish to mulloway. Australian salmon and trevally; in some estuaries, even the chance of a trout. All fun to catch and some more challenging than others. Enjoy catching that toadfish when targeting bream. Like riding a scooter, it’s fun – just don’t tell your friends you did it. A bend in the rod is better than none.

You can expect a variety of bycatch when targeting estuaries. Most, if not all of these fish eat the same food, and our flies match it. I get excited about the diversity of an estuary catch or bycatch, just as I do when hooking a redfin or accidentally snagging galaxias fishing for lake trout.

Enjoy the bycatch – a little salmon is still a lot of fun to catch.

Most estuaries share the same basic characteristics. Freshwater flowing from mountains or hills, then snaking across the flats into a lake or river, before finally meeting the ocean. It’s this last bit we’re interested in, the bit where the river channel is effectively at sea level. Here, freshwater from rivers and streams mixes with saltwater from the ocean. Just as trout streams can vary from weedy, near flowless Monaro creeks, to roaring high country torrents, estuaries too come in endless shapes and sizes. In southern Australia, estuaries may be 50 kilometres long or a tiny 50 metres. The mouths of estuaries, leading into the ocean, can be closed, partially open, or deep and wide enough to allow ships through. All different, but all holding fish.

Winter evening on the Gellibrand.

Start at the end

A great place to begin your estuary flyfishing journey is at the end. By that, I mean the end of the estuary, where it meets the ocean. Many large estuaries have towns built around them; for example, Melbourne, Warrnambool and Mallacoota, just to name some major ones. This means there’s easy access to the mouth of these estuaries. Roads, boardwalks even dog beaches if you’d like to bring your best mate along.

Estuary mouths or entrances vary a lot, but that mixing point can be great for access, wading and casting (like surrounds with lots of nice open sand), and their characteristics can encourage concentrations of active, feeding fish. The Barwon River estuary has a lake at the top (Lake Connewarre) contributing to near constant – and often very strong – tidal movement as this upstream lake ‘basin’ constantly empties and refills. Meanwhile, estuaries such as Bemm River or Mallacoota Inlet, have lakes further down towards the mouth. This means less water pushing past the estuary channel or mouth. At the far end of the scale, many estuaries, even quite large estuaries, can be closed to the sea at times, meaning little or no tidal flow to contend with.

Estuary mouths usually offer easy access and plenty of room for the back cast!

Entrance tactics

If starting out on your estuary journey and you don’t have a boat or kayak, look at the last section before the entrance. Away from the mouths, you may find bank and wading access limited by scrub, snags, reeds or cliffs – all of which are perfect to cast at from a watercraft, but difficult on foot. Moreover, some systems stretch for miles without roads or access, making entrances the most viable land-based option. I should note that not all estuary entrances feature easy foot access, with a few East Gippsland systems like the Bemm River (where a boat is needed) being the exception. Nevertheless, for most estuaries, heading for the mouth is a good start.

First up, concentrate on sand flats closer to the ocean. Any rocky edges and weed-beds are particularly likely spots. Using floating lines, cast at any hole in the sand, channel or drop-off, or at any log or rock bar. Sometimes the drop-offs or holes can just be a different colour. A touch darker or different shade of sand. Any difference in water depth across these flats will hold food and often, the fish feeding on it. For both predator and prey, these spots are a great place to hide when away from the depths of the main river or lake.

Rocky edges are good spots to target.

Even one single stick stuck on the bottom, or a small weed clump is good for a few casts. Anything different that stands out is worth a look or a cast. There are often very large areas of sand flat out there, but not many spots to hide.

Entrance flies & fish

The relatively shallow water around the entrance zone favours surface flies such as Disco Shrimps or small poppers, through to unweighted BMS patterns and bead-chain shrimp style flies. A point to make here is to bring your trout box with you. There’s no better small baitfish pattern than a stripped Magoo or Woolly Bugger; flies with plenty of inherent movement like a marabou tail or hackled bodies. Even Zonker-style patterns like Green Machines and Cat Flies can work well.

Fish to expect in these circumstances include sand whiting through East Gippsland and the NSW South Coast, which eat aggressively, then throw in long runs and dancing jumps. More broadly, add flathead, growing up to and over 1m in length (though mostly smaller). Luderick are a strong fighters which will eat a shrimp fly and even a popper – not just a weed fly as commonly believed. Add Australian salmon – a great looking and hard fighting sport fish – and silver trevally, which pull as hard if not harder. And of course bream, arguably the perfect estuary fly species and found in just about every system from Docklands to the East Gippsland wilderness. Fishing closer to the ocean obviously means more salt, which a lot of these fish prefer.

Estuary perch are one of my favourite species.

Around wintertime, we find more fresh pushing down the systems. Certain fish, such as schooled-up estuary perch, follow the fresh closer to the ocean to find the right salinity. The Blue Hole near the mouth of the Hopkins River is a great example of a land-based fishing location for these schooled-up perch, with a large numbers of bream and salmon often present to target as well.

When it occurs on the incoming tide (as shown in the video), the area where seawater meets the fresh/ brackish estuary water, is often a real hotspot and worth following as it moves upstream. This applies to all estuaries.

Shallow at first…

In many estuaries, an appropriate approach would be walking the flats near the entrance. Starting off shallow and careful so as not to spook fish that may be ‘tailing’ for crustaceans, baitfish and sandworms. Sight-fishing is a great option on the right day. Try a popper-style fly in one to five feet of water with inch long strips to cause a pop or bloop. There’s nothing better than a surface eat! Watch for bow-waves chasing your fly. And keep your eye out for dig holes in the sand where fish have been feeding. These are a dead giveaway you’re in the right spot.

Dig holes on a Hopkins River flat – a sure sign that fish hunt this area.

Depending on what part of the south you’re in, look for flathead lies: indentations literally the shape of a flathead. Flathead will follow the tides in and out of the shallows, mostly sitting on drop-offs waiting to ambush prey… and your fly. If you find these vacant lies in the shallows, it means the flathead have just moved out a touch deeper: a perfect place to tie on a Clouser to bump the bottom. Or other shrimp and baitfish patterns. Don’t forget though, flathead, especially dusky flathead, love a surface fly. They also have a scary set of fangs, so if targeting duskies, up your tippet size. Off the surface, they have an eat I can only liken to a Murray cod.

… Then deeper

Once you’ve fished the shallows you can wade in a touch deeper, finding the main river channels or deeper holes. Now try to get your fly as close to the bottom as you can… but also with as light a pattern as you can get away with. While that sounds contradictory, a slow sink is a lot more natural than a fast sink.

So, work your way through your fly weights from bead-chain eyes to dumbbell eyes. This can also be the time you think about using sinking fly lines. I like sink tips for land-based flyfishing, as you’re running line isn’t sinking at your feet and getting caught on everything. One good option here is using sinking leaders. A loop-to-loop connection can turn your floating line into a sink tip. You can also extend leaders and tippets to allow for the required sink rate. (Full sink lines in different sink rates are a much better option from a boat.)

Covering a likely snag from the boat.


As with trout fishing, fish your flies in a way which matches the pattern you’re using. Small strips and long slow draws for a shrimp pattern. Sharp strips with pauses when fishing a baitfish pattern.

Bonefish-style flies such as the Crazy Charlie or CXI Special work well in bonefish-free southern estuaries using long draws and long pauses. The wing of these flies, tied with craft fur, Arctic fox or Finn raccoon, stands up straight, dancing in the water. Sometimes it suggests a sandworm or slowly swimming shrimp.

Bonefish flies still work during a southern winter!

But no hard rules. Change the retrieve if it’s not producing a bite: slower, faster; more or less twitchy, longer pauses…

Moving into summer

In the warmer months, we find fish a lot more spread out through these systems due to less fresh flowing down. The same techniques, just further up and down the rivers and lakes.

Grassy reed edges and undercut banks are perfect spots to look. Submerged logs and rock bars. Try to think like a fish. They’ll want to hide or be where the food is. Go back to shallow water in low light conditions and/or early morning and late afternoon.

Risk/ reward: putting the fly close to fish-holding structure can end in a snag… or a good fish.

An incoming tide is a good time to target the shallower margins, with fish coming out of the deep drop-offs to feed over the freshly-submerged grounds. A little later, the outgoing tide is perfect to fish the drop-offs, with small baitfish and crustaceans forced to follow the receding water into the deep. Hopping your fly off the bottom and up the drop-off, or down the drop-off, waiting for those fish in ambush.

As mentioned before, many of these inlets and estuaries become landlocked at times, with drifting sands closing the entrance mouths. In fact, some are almost permanently closed, with only floods, big seas or king tides breaking their sand bars.

Once again, a ‘dammed’ estuary gradually floods the margins and just like on a slowly rising trout lake, these flooded margins are well worth plenty of casts. A variety of species will take advantage of the new feeding grounds, and like trout, it will surprise you how shallow they will come in to feed. Newly covered rocks, trees, snags and reeds will all hold fish food.

When blocked from the sea, ‘flooded’ estuaries can present their own opportunities.

Start in winter, stay for summer

Without the distraction of the trout streams, now is the ideal time to start your estuary journey. Once you do, you might find (like me) that you’re drawn to this salt/fresh challenge at any time of year.

Gippsland wilderness.


Use a 6 weight rod from 9 to 10 ft with a floating line, and a sink tip option when needed. Floating line leaders should be about 9 ft with around 4 ft of tippet tied on.

Tippet from 4X through to 1X will cover most estuary species. Fluorocarbon is a must due to its abrasion resistance – lots of estuary fish like running you into rocks, jetty pylons or any snag.

Up tippets when targeting big flathead, mulloway or any larger fish – a good option is tying 12lb to 20lb straight to your fly line.

Don’t be too confused about estuary flies. Stacks of patterns work, including many trout flies. Just be sure to carry a range of weights and sizes.

If you’ve got a rod & reel set-up with saltwater tolerant components and a sealed drag, great! After every session, I’d still recommend washing with freshwater. If using your freshwater gear, again great! Just make sure you wash all the salt off after each day on the water. Personally, I tend to fill the bath up and wash both my flies and rod set-ups after each trip. Take care of your fishing gear! 

Once the weather warms up, wet-wading becomes an appealing estuary option. However, I always keep a pair of shoes in the boat or on my feet for walking the flats or inlet edges. Sharp rocks, oyster shells or stingrays can ruin a fishing trip pretty quickly.