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.

Snorkeling spots in Lee County, Florida (Bonita Springs, etc.)

Snorkeling Estero Bay from the East side of the road at Bonita Beach Dog Park.


Folks who know I'm a marine biologist often ask me if I can recommend any good, nearby snorkeling spots. (Within the Naples / Bonita Springs / Estero / Fort Myers / Sanibel area.) The answer is YES I CAN- SORT OF.

The thing is, this part of Florida doesn't have any near-shore coral reefs, and the waters are often dark and murky from a combination of natural and man-made factors like stirred-up mud, tannins, and blooms of microscopic algae that feed off the high levels of nutrients in the water. So even where there IS cool underwater life to see, you often can't see it very well because of the poor water clarity. Having given those disclaimers to set expectations appropriately low, I have had some good snorkeling experiences around here, and I'll tell you where your best bets are to have some good experiences yourself.

General recommendations-

1. Best times are weekday mornings before there is much boat traffic to stir up the water. Boats can also run over you and chop you into little giblets of meat with their propellers. So you should bring a dive flag if you're going in an area that potentially has powerboats.

2. Best times are when it hasn't been too windy / wavy, because wind makes waves and waves stir up mud from the bottom that reduces the visibility. Winds less than 10 knots are usually OK. That said, you can get away with snorkeling when it's windier if the winds are OFFSHORE WINDS. That means winds blowing from the land out to sea. These will not make waves along the shoreline, so they won't stir up the water.

3. Tide (level and whether it's coming in or going out) matters. Particularly when you're near the mouth of the estuary, where there's a changing mix of fresher estuary water and saltier ocean water, you may get the best water clarity when the tide is coming in, bringing the more clear water from offshore in the Gulf of Mexico. However, if there have recently been a lot of waves in the Gulf of Mexico from West winds, the incoming tide won't help and it could actually be more clear further back into the estuary. Tide can also matter because some sites may be too shallow at low tide or too deep at high tide.

Specific sites-

Estero Bay- Estero Bay is a shallow, semi-enclosed body of water where fresh and salt water mix. It has some interesting sea bottom habitats including beds of seagrass and seaweed that often have snails, fish, sea urchins, anemones, crabs, and other organisms living in them. The trick is to find a seagrass bed accessible from shore, in an area where the water isn't too murky. I have had some luck going from the east side of the road at Bonita Beach Dog Park on Lovers Key.There's a shallow area with seagrass, and a deeper channel as you go south towards the New Pass bridge that has some oysters and other shells and often has interesting crabs, urchins, and fish like Mangrove Snappers and Sheepshead.

A sand perch hanging out by a clump of oyster shells in the deeper channel part.




Another site at Estero Bay that sometimes works is the Big Carlos Pass beach access at the north end of Lovers Key. Big Carlos Pass is the biggest opening from Estero Bay into the Gulf of Mexico, and it sometimes has pretty clear water on an incoming tide. The bottom there is shelly, and there are some big pieces of rubble further out, like concrete pipes, that are covered with sponges, seaweed, and sometimes soft corals. Underneath the Big Carlos Pass bridge, around the pilings, there are piles of concrete blocks that often have reef fishes swimming around them. Just watch out for fishing lines and boats.



The ocean side of Lovers Key can also work for brave snorkelers if the tide is slack or outgoing and there are no waves. Near the entrance to Big Carlos Pass there is kind of a deep channel between shore and an offshore sandbar, and the sand is scoured away from the bottom there revealing rocks with urchins, seaweed, and sometimes big fish. You can swim really far out from shore and still in be in shallow water over the shifting sandbars. Watch out for boats, though.



San Carlos Bay- San Carlos Bay is the crossroads of several estuaries in the more northern part of Lee County. It's where the Caloosahatchee Estuary meets Matlacha Pass and Pine Island Sound. The toll bridge to Sanibel Island (the Sanibel Causeway) crosses San Carlos Bay and includes two man-made islands where you can pull off and park to snorkel or windsurf or picnic or whatever. Look at the area on Google Earth and pick a spot where you see dark, mottled patches near shore. Those are seagrass and seaweed beds with a mixed shelly / sandy bottom. Depending on which direction the wind is coming from, different sides of the different causeway islands may offer the best shelter from the wind and waves and the most clear water.



If you want to snorkel in a similar environment but don't want to pay the $7 toll for the Sanibel Causeway, you can pull off on the side of the road just before the causeway at San Carlos Bay beach.



Another interesting spot is Bunche Beach, which has a mix of seagrass, seaweed, sand, rock/shell and invertebrates like sponges.



Good luck exploring, and if you make any great snorkeling discoveries, please share them in the comments.

FL Keys Marine Lab field trip, Spring 2018

Every semester I take my FGCU Marine Ecology class to the Florida Keys Marine Laboratory for a few days of educational snorkeling. I bring lots of marine life guidebooks and encourage the students to identify all the organisms they see. I think learning what species you're looking at is the first step towards assessing the state of the ecosystem. It's also something I enjoy as a hobby, so I really look forward to photographically "collecting" new-to-me species.

This year I "scored" a few species that I was particularly excited about: Ocellate Box Crab, Batwing Coral Crab, Golfball Coral, Barred Hamlet, Reef Butterflyfish. You can find them and lots more, with descriptions, in the album of all the pictures I took this year, which is posted on my science facebook page.


The next part of this post may fall into the "too long didn't read" category for some people, but I felt like I should share these impressions about how the underwater habitats in the Florida Keys are doing lately, what with Hurricane Irma and some man-made problems, as well. Below is a summary of the changes I've seen at five of our regular snorkeling sites.

Site 1- KML Cove. The Keys Marine Lab is on the shallow, sheltered waters of Florida Bay. We do our first snorkeling activity in a little cove behind the lab. The cove has lush beds of seagrass and algae, with a few sponges and small, inconspicuous corals. I haven't noticed much change in the cove since Irma, besides some sunken branches and debris. However, there have been major impacts further north in Florida Bay, where lots of seagrasses died out due to salinity changes, murky water, and algae blooms. While boating through the Bay this spring we hit a line of the "post-Irma bad water," which was olive brown and totally opaque. Damage in Florida Bay can have a harmful domino effect, because when seagrass dies, it releases nutrients that cause algae blooms, which cause more seagrass to die, which releases more nutrients, and so on.

Site 2- Zane Grey Creek. This is a mangrove-lined, tidal channel that drains Long Key's shallow, internal lagoon. The creek waters can be tea-stained with tannins from seagrass and mangrove detritus, but they are generally fairly clear and high in salinity. Strong ebb-tide and flood-tide currents through the creek, coupled with its stable, high salinity, allow for the development of rich communities of filter-feeding organisms on the mangrove roots. In past years, sponges of all sorts- purple, blue, orange, white, brown, green, etc., covered the mangrove roots, and truck-tire sized loggerhead sponges studded the creek bottom. Those ALL died after Irma. Every single sponge. We speculate that they were done in by a combination of fresh water from the extreme rains, and the choking clouds of brown silt that were suspended in the water all around the keys in the weeks after Irma. I thought some sponges might recolonize the creek between November 2017 and March 2018, but they didn't. KML staff said that something similar happened in the creek after Hurricane Wilma in 2005, and it took about 7 years for the sponges to recover.

Site 3- Cheeca Rocks is a "patch reef" in shallow water relatively near the shore of Islamorada. It's designated as a Special Protected Area (SPA), which means that there's no fishing or collecting allowed there. It's unusual for a near-shore reef in that it still has a relatively high percentage of living hard corals, including the massive brain corals and star corals responsible for building the rocky structure of the reef. Since I first visited Cheeca Rocks in 2012 it has suffered from coral bleaching and disease outbreaks, which have killed or partially killed a substantial portion of the coral colonies. For example, some types of brain coral and maze coral are no longer present there. That said, Irma didn't seem to kill any corals at Cheeca Rocks that weren't already dead before the storm, although it did tip some colonies of star coral on their sides, and it moved sand that partially buried or un-buried portions of the reef. The main difference I noticed at Cheeca Rocks between November 2017 and March 2018 was a big increase in the amount of macroalgae (seaweed) on the reef. The algae and other soft-bodied organisms were probably blasted away by Irma's waves, but later took advantage of the vacant real-estate to recolonize. Algae compete with corals for light and space, so too much algae can harm reefs, especially if its growth is fueled by excess nutrients from pollution, or if the reef lacks algae-eaters like parrotfish and urchins.

Site 4- Alligator Reef. The saddest reef site, ironically, was the furthest offshore one that ought to be the most pristine and beautiful. Alligator Reef is a SPA like Cheeca Rocks, so it does have a lot of fish. It just has very little hard coral. Less than 1% of the sea bottom there is hard coral, whereas on a healthy reef it should be >30%. When I first visited Alligator Reef in 2012 there were at least a few colonies of hard coral studding the reef top. Those colonies included one endangered Elkhorn Coral, a remnant of the forest of Elkhorn Coral that covered most of Alligator Reef before it began dying off in the 1980s. Even though the reef was basically "dead" before Irma, inasmuch as it didn't have enough hard coral cover to keep its mineral growth rate apace with the rate of erosion, it at least looked pretty because there were lots of soft corals, sponges and algae on the reef skeleton. Irma swept those organisms away, highlighting the reef's depressing desolation. In November 2017 Alligator Reef just looked like a dusty concrete ledge. Since then the fast-growing algae have recolonized, and some of the soft corals and sponges are beginning to recover, as well. The hard corals really seem to be gone for good, though, which is crazy and awful.

Site 5- Stag Party. Staghorn Coral is a relative of Elkhorn Coral. It looks like deer antlers. It used to be one of the most common corals on Caribbean reefs, but it started dying out along with Elkhorn Coral in the 1980s. The "Stag Party" snorkel site was one of the few places where one could still reliably find Staghorn Coral in the 2000s, but bad bleaching and disease events in 2014, 2015, and 2016, related in part to mismanagement of water flow to the Everglades and Florida Bay, have almost completely wiped it out. I snorkeled the site for about 30 minutes this month before I found even one remnant patch of sick and pale looking Staghorn Coral. There have been big hopes that this potentially fast-growing coral will make a comeback, but I don't think it will happen unless we take big steps to fix our water pollution and climate change problems.

I'm Married - Woo Hoo! + Snorkeling Videos

About three years ago I met Rhonda Mason on a date in downtown Boston. I knew almost instantly that she was the one for me, but it naturally took some time to convince her that I was the one for her. When we were dating, Rhonda helped me find my current marine biology professor job in Florida. After I interviewed and got the job I asked her to marry me and move South. She said yes! We were fiances for two years, then on the 21st of June, 2014 we had a big, wonderful wedding near her hometown in New Hampshire. I am SO HAPPY!

For our honeymoon we decided to do it by car, since we already live in the tropical paradise of Florida, and we could take more water toys with us that way. (Shortly prior to the wedding we had replaced my red rusty minivan with a fresh blue minivan with working AC - luxurious!) The first couple nights we stayed at the Hampton Inn at Manatee Bay, Key Largo. In seagrassy Tarpon Basin behind the hotel is where I shot this snorkeling video. We also snorkeled on the reefs near Key Largo from the charters at Pennekamp State Park.



For the second part of the honeymoon we stayed further west at Parmer's Resort on little torch key (see hammock picture).

We snorkeled near shore at Bahia Honda State Park, on Looe Key Reef via a charter boat, and at Fort Jefferson after riding out to that Historic Fort island on the Yankee Freedom II ferry. This video, mostly shot by Rhonda is a compilation from all our reef snorkeling trips.