Manatees to oysters; school's out fieldwork blitz in SW Florida

I finished my spring semester grading on Sunday night then woke up at 6 am Monday to begin four consecutive days of benthic ecology fieldwork in the Caloosahatchee River Estuary (CRE) and Pine Island Sound (PIS). Here's a little about the projects:

CRE- Caloosahatchee means "river of the Calusa;" named after the people who lived in SW Florida prior to Spanish and English colonization. The original headwaters of the Caloosahatchee were west of Lake Okeechobee, but in the 1880s a canal was constructed to extend the river to the lake itself. This seemed like a good idea at the time, providing a highway for steamboat traffic and a mechanism for controlling lake level to allow more farming around its shores. Three locks and dams were also added to the Caloosahatchee to retain or release water as needed for human use, turning the river into a linear reservoir. Ecologically it was a disaster, of course, because it starved the Everglades of water and turned the relatively clean, steady flow of the Caloosahatchee into a wildly fluctuating, polluted flow.

From the Gulf of Mexico to the first dam on the river, life in the CRE now suffers from salinity levels that flip-flop between high and low extremes beyond the natural variability of an estuary. (I wrote a paper about that with some other scientists in 2020.) In recent decades we have tried to regulate the flow to better meet both nature's needs and human needs as part of the massive "Comprehensive Everglades Restoration Plan" (CERP). The latest Lake Okeechobee Systems Operating Manual (LOSOM), integral to CERP, is better at keeping water flows to the estuary within ecologically reasonable bounds. It's not perfect, though, and in high rainfall times or droughts like we're having now the estuary still gets too fresh or too salty.



The best "ecological indicator" of the estuary getting too salty is loss of the Tape Grass (Vallisneria neotropicalis) beds that used to cover large areas of the upper estuary. Vallisneria is a freshwater plant but can tolerate salinity levels up to about 10 ppt (pure freshwater is 0 ppt and the ocean is 35 ppt). So the upper parts of estuaries are OK for it. We want Vallisneria growing in the CRE because it provides food for wintering manatees and habitat for fish and crustaceans. It also helps absorb some of the excess nitrogen and phosphorus getting into the estuary from urban and agricultural pollution, and benefits seaward habitats like seagrass beds by preventing algae blooms. (My grad student Brondum Krebs and I wrote a paper about that in 2024.)

Picture of extensive Vallisneria beds in the CRE in 1984, taken by Calusa Waterkeeper emeritus John Cassani.

There have been various governmental and non-profit environmental group efforts in the 2000s to restore the mostly-lost Vallisneria beds, including an ambitious planting effort begun in 2024 using cages to protect the plants from grazing while they're getting established. Seagrasses (and their freshwater kin like Vallisneria) often experience "positive density dependence" in stressful environments, meaning they flourish when there's enough of them around that they can stabilize the local environment and resist grazing, but if they fall below that self-sustaining threshold it's really hard to get them back. Getting them back may require both a big reduction in the environmental stresses and active measures like planting. The 2025-2026 drought in Florida has greatly worsened the salinity stress on naturally recovering and recently replanted Vallisneria in the CRE. This week we were encouraged to see SOME Vallisneria still living in the CRE restoration areas that we monitored, but there was much less than there had been just 6 months ago.

A Vallisneria hanger-on.

There were also some upsetting signs of trouble in the upper estuary such as:

1. A huge, rotting manatee carcass in one of our monitoring sites. This may be a late casualty of the February power plant snafu that cut off the warm water flow that manatees were sheltering in on the Orange River, a tributary of the upper CRE. Or it migth have been a boat strike, since the seasonal speed limit for boats expired on March 31st but some manatees are still hanging out in the upper CRE. I'm not sure what the manatees are still doing up there because there's very little Vallisneria for them to feed on. They might be eating the filamentous red algae Polysiphonia subtilissima, which is abundant in the upper estuary due to the nutrient polluted conditions. Compared to true plants like seagrasses and Vallisneria, algae are thought to be an inferior food for manatees, so this is a little worrying.

2. Oysters, Crassostrea virginica, far further up the estuary than I've ever seen them before. Oysters prefer water of 14-28 ppt so they're usually in the middle to lower part of the estuary, rarely even making it as far up as downtown Fort Myers. This week we actually found a couple of oysters upriver of the railroad bridge and "Beautiful Island" water quality sensor maintained by the Sanibel Captiva Conservation Foundation (SCCF).

Oysters cement their shells to whatever hard substrate is available. In the upper CRE the hard substrate is shells of Rangia cuneata and Polymesoda caroliniana clams, which are normally the dominant bivalves in that low salinity zone.

Over the last 90 days the SCCF sensor has shown salinities near and sometimes exceeding 10 ppt, which is really bad for Vallisneria. A lot of the Vallisneria restoration areas and former strongholds are well seaward of Beautiful Island and have surely experienced even higher salinities this year.

What should we make of this? Should we give up on trying to restore Vallisneria in the Caloosahatchee, since climate change, sea level rise (about 30 cm [1 ft] since 1965), and increasing human demands for fresh water are going to make it even harder to maintain low salinities in the future? We need to be realistic, but I don't think we should give up yet. A huge reservoir (the C-43 reservoir) has recently been built upriver on the Caloosahatchee to store water in wet times and gradually release it in dry times. We didn't need that kind of artificial thing back in the day because natural wetlands in the watershed would store and slowly release water to the river. However, our drainage of the wetlands with canals, and other watershed modifications like pavement and rooftops that prevent groundwater recharge have made it necessary. Once it's full, the C-43 reservoir should at least buy us a couple decades of keeping the seawater at bay and maintaining a low salinity Vallisneria habitat.

There is the issue of the water in the C-43 reservoir possibly becoming a polluted soup of algae unsafe for release, since it's built on top of defunct orange groves with fertilizer-saturated soils and doesn't include any artificial wetland features for nutrient removal. But we'll cross that bridge when we come to it, I guess. I like the idea of having some kind of floating aquatic plant harvesting system in the reservoir to sponge up and repurpose the excess nutrients until the water is clean. Another thing we should be working on for the real long term is an inland retreat for the Vallisneria, because at some point sea level rise is just going to be too much to keep it growing where it's hanging on now. That inland retreat thing is something that both humans and plants will be going through in the next couple centuries.



PIS- Pine Island Sound, in contrast with the beleaguered pollution-highway that is the main stem of the Caloosahatchee Estuary, is the healthiest estuary in SW Florida. This is because its watershed is relatively sparsely populated barrier islands with decent pollution controls, it has good connections to the Gulf of Mexico through tidal inlets, and only gets a moderate amount of spillover pollution from the more inland estuaries like the Caloosahatchee and Matlacha Pass. PIS is not perfectly healthy, though. For example, it lost its Bay Scallop population after the construction of the Sanibel Island causeway bridge, which reduced flushing of the estuary and caused it to take on more gunky Caloosahatchee water. From north to south Pine Island sound you can see a definite transition in water color from Caribbean blue-green to more Caloosahatchee brown.



The reason I was in PIS on Thursday was to help with "ground truthing" for a seagrass mapping effort led by the South Florida Water Management District. A few months ago a contractor for the SFWMD flew over all the SW Florida estuaries aquiring detailed imagery for seagrass delineation. This is an important effort that's repeated every few years to track seagrass gains and losses. It gives us a report card on our environmental stewardship, because seagrass beds expand where water quality and salinity levels are good, and they perish where water quality or salinity levels are bad. I was nervous about the PIS ground truthing because I'm only a so-so boat operator and navigator, and the geography of PIS is a complicated maze of islands, vague channels, and dangerous shoals. To make up for my ineptitude I pre-scrutinized maps of the area and carefully planned a zig-zagging route to hit all the spots I'd been assigned to check. I had sharp crew of FGCU graduate student Alvio Barbaretta and undergrad Bailey Day, who made sure I didn't get lost on the drive to the boat ramp, measured water clarity, punched in coordinates and data, and kept eyes out for hazards of the sea.

This allowed me to focus on the fun stuff like snorkeling around the boat to see what species of seagrasses and algae were present. After three days in the coffee-brown water of the upper CRE with barely any submerged vegetation, the lush seagrass meadows and blue-green water of PIS were wonderful.

We even had a close encounter with LIVE manatee who seemed happy, and very curious about our boat.

Every site we stopped at in PIS had seagrass, though it was sparser at deeper sites (a result of reduced light availability) and it was more algae covered at southern sites (a product of more nutrient pollution) from the Caloosahatchee. As bad as the drought has been for Vallisneria in the upper CRE, it's actually pretty helpful for the saltwater-associated seagrasses in places like PIS, because less river flow and runoff means less delivery of coastal pollution. The beautiful seagrass scenes from Pine Island Sound are not something that we should take for granted, but rather, something that should inspire us to be better stewards of all waterways in Florida.