Top 10 Tips for Mosquito Lagoon and Indian River

If you want to be successful fishing the Mosquito Lagoon and Indian River systems then listen up. Backwater Fly Fishing is bringing you our top 10 tips featuring the information you need to be successful on the flats.

If you find find these tips helpful, feel free to share them with your local fishing buddies. Lets get started!

#1 Clean water makes the fishing hotter!

Finding clear water in the lagoon while sight fishing is important for the obvious reason of increased visibility; however, lets look at a few more reasons why clean water is important!

The number of the large algae blooms that have occurred over the past years have choked out a majority of the naturally present sea grass beds. This happens due to the algae sucking up oxygen and removing nutrients, but mostly because of its ability to rob the other vegetation of much needed sunlight. Screen Shot 2016-07-05 at 1.30.09 PMFinding areas with clear water typically means a higher oxygen level is present, allowing fish species like redfishsnook, and sea trout to feel more at home in that area. Baby tarpon on the other hand seem to be just fine in the darker water as they will regularly breach the surface in these areas to satisfy their oxygen needs.

If you find a good bait source in clear water then it is worth sticking around and seeing what predators show up.

#2 If it is hot outside, then the saying, “The Early Bird Gets the Worm” could never be more true.

The heat of summer on the Mosquito Lagoon and Indian River can put a lot of stress on the anglers as well as the fish. With temperatures souring often into the triple digits it is important to understand the ways the heat will change how and when the fish feed.

Since the cooler temps take place during the first hour and half of day light, fishing early and later in the afternoon will be what the majority of anglers are trying to do. This is typically when actively feeding fish will be present in the shallowest water, making them perfect targets for sight fishermen.

Getting there early and being quiet will be your best advantage in bagging a few fish before the sun breaks the horizon.

#3 Look for flowing water

Since the Mosquito Lagoon and Northern Indian River are not typically effected by the tide, flowing water is usually a goldmine. While flowing culverts and creeks can be found throughout the year, targeting these areas in late August and thru September is usually the best.

After the summer rains have filled up the back ponds, creeks, and mosquito ditches the management agencies tend to open up the many culverts that surround the lagoon and river system. These are areas that always attract fish.Screen Shot 2016-07-05 at 1.40.32 PM

When fishing these areas be sure to try a few different approaches.Redfish, snook, sea trout, ladyfish and baby tarpon all use these areas to hunt and feed throughout the day. Tossing one of our Ostrich Clouser Minnows or Poppin’ Flats Shrimp in the current will usually produce a solid strike.

Note: All the fish below were caught in the same afternoon while fishing culvert pipes.

#4 Know your boat ramps

The Mosquito Lagoon and Indian River systems are filled with easy access points for both kayaks and skiffs. Knowing where these boat ramps are in relation to where you are hoping to fish will help you decrease the amount of time you spend running over other potential fishing areas as you run 8 miles north from biolab just to fish a flat. Don’t be that guy!

Talking with locals, looking on google earth, and even reading a few road signs will help you find the boat ramp best for you on that particular day.

This brings us to our next tip…

#5 Buy the ‘Top Spot‘ map for gosh sake!

The Top Spot map for the Mosquito Lagoon and Indian River systems is a fantastic resource for a number of different reasons. One of the benefits to these maps is the clearly marked boat ramps. If you have not looked at a top spot map, here are a few reasons you should own one.

  • They are made by guides that have fished the area for years.
  • They give GPS coordinates and clearly mark what tends to be the best fishing spots in the area.
  • They mark water depth, obstructions, and even list the type of bottom you are likely to encounter in each area.
  • They tell you what species of fish will visit each area depending on the time of year.
  • They are deadly accurate in most cases, but suggest to give some slack to possible changes in terrain and water depth.

#6 If your spot is blown out and all you see are mullet, move on

While fishing during or on the backside of a strong algae bloom it is important to have a backup plan. Often you will pull up to a spot that you fished the day before, and you will find it completely blown out and discolored. If there are feeding fish visible then fishing that school would obviously be worth your time.

However, most often the fish will move out of those areas and look for the cleanest water possible. I suggest you do the same. Don’t waste valuable time in an area that is not likely holding fish that day. It is ok to move on to the next spot or activate your ‘plan B’. Oh yeah, make sure you have a ‘plan B’.

#7  Talk to the folks at Orlando Outfitters for a quick update

The guys at Orlando Outfitters are a huge resource to have in the area. Their shop offers all the gear, materials, and fly accessories that you will need to be successful on the local waters.Screen Shot 2016-07-05 at 1.48.59 PMIn addition to their great shop, each employee is knowledgable about the current status of the lagoon and river system. If stopping buy and chatting is an option then it is what I would recommend doing. If you do not live in the area then a quick phone call will be all you need to get a rundown of what has been going on in the fishery for the past few weeks.

This information can be critical to formulating a plan. You can find more information about the crew and contact info at

#8 If you find some good grass and clear water, hang out for a bit and see what happens

We talked a little bit previously about how important it is to have a game plan when fishing the lagoon system, and how important it is to know when to move on when your favorite spot seems to be void of fish. This next tip goes hand in hand with those two points.

When moving to the area you are trying to fish it is important to look for areas with clear water and a grassy bottom that you didn’t know where there. These areas are often places people overlook and can be holding fish.Screen Shot 2016-07-05 at 8.08.18 PM

If you happen to locate an area similar to this, stop and sit quietly for 10-15 minutes to see what pops up. More times then not, you will be delighted by what you see.

#9 If you see heavy boat traffic then go some place else

Like most waterways in the area the lagoon and river system can be crowded in certain areas depending on the time of year, holidays, or even just weekend traffic. If you enter your favorite spot to find a few boats working up the flat…MOVE ON! Don’t waste your time fishing over an area that you know just got hit hard.

But more importantly than that, don’t be rude and cut in on another boat who obviously got up earlier than you did that morning to be the first one on the flat. Simply nod, wave, or tip your hat as you move on to another spot.

#10 Spend the money for some good specs

If you have been sight fishing for any amount of time it should be obvious how important quality sunglasses can be. I am not saying you have to drop 300 bucks on your favorite pair; however, I am saying that not purchasing a quality pair will weaken your ability to see that trophy fish out of the corner of your eye. If you are a guide, your job depends on this.

Screen Shot 2016-07-05 at 8.24.17 PMDon’t expect the kmart special to get the job done like these guys will on the water.

If you want to stay up to date on posts similar to this, hd fly tying videos, and videos our local and destination trips, be sure to LIKE  Backwater Fly Fishing on Facebook.

Keep your hearts right, and your lines tight!

Capt. Jesse Males

2 Comments Add yours

  1. Chris says:

    You stated above algae suck up oxygen and nutrients which are needed for plants to survive. Both algae and plants utilize co2 to PRODUCE oxygen via photosynthesis. They do not need oxygen for growth. Instead, what is likely the source of plant death in the presence of algae blooms is inadequate sunlight, another component in the photosynthetic reactions, due to occlusion of the water. Otherwise good article.


    1. You are correct about that. Thank you for pointed that out.


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