It has been quite some time since I went fishing just to catch fish. Or, judged the quality of a fishing day by the number of fish in the box. Good thing, considering the lackluster days I’m tending to have on the famed, yet defamed, Indian River Lagoon (IRL). Black, polluted discharge from nearby canals keeps me bummed out. Only on the incoming tide near a major inlet, such as the Fort Pierce Inlet, do I typically find the pretty green water that normally equates to good fishing in the Lagoon.

Other experienced guides feel the same way. Though we are not trained scientists, like many seasoned anglers and watermen in general, my fellow guides can tell when the water and the habitat looks right, or if something is amiss. We take in the whole scene — water clarity and color, presence of bait, and the appearance of the bottom. I always note the number of birds, diversity of bird life, and other wildlife. Trip after trip, I sense the health and vitality of these estuaries — the cradles of almost every fish we value as well as the species they eat — declining steadily.

Here’s the situation. The Indian River Lagoon Complex is a shallow, expansive ecosystem including three lagoons covering 161 miles along Florida’s East Coast. The IRL is an “estuary of national significance” and an aquatic preserve. It is home to over 2,100 different species of plants and 2,200 species of animals, including 700 fish species. Several major rivers and creeks flow into it, including the iconic St. Lucie and Sebastian rivers. In more pristine states, these watersheds usually supplied the rich mixing zones known as estuaries with the healthy levels of clean fresh water, when it’s most needed, to encourage all kinds of valuable activity: from ensuring healthy seagrass meadows and abundances of shellfish and crustaceans, to promoting plenty of forage fish species that adult predators must have to grow and reproduce.

“Thanks” to a labyrinthine system of man-made canals and other flood-control devices designed first and foremost to keep crops, streets and lawns irrigated and above water, and to the pollution from septic tanks, these estuaries are alternately deprived of clean fresh water or impacted by nutrient-laden runoff. In the case of the St. Lucie River, we experience discharges of filthy water that is measured in millions and sometimes billions of gallons. Over more than half a century of rampant development and exploitation, the lagoon put up a great fight. But over the past few years, we’ve witnesses a lagoon-wide drastic decline in seagrass coverage, and alarming changes from seagrass flats to flats that are either barren or covered in macroalgae. Scientists estimate that some 47,000 acres of seagrass were lost, which economists value at $5000 to $10,000 dollars per acre. So our local economies are losing $235 million to $470 million for each year the grasses remain absent — a fact evidenced by my own tax returns. Up and down the lagoon, businesses like mine have fallen off substantially. There are days when I wish I had a boat big enough to guide offshore.

Thanks to several important conservation measures implemented in the last decade or so, my friends in the charter industry that fish offshore seem to be enjoying a rebound. Though it seems like the system’s science-based annual catch limits and protected areas adopted by the South Atlantic Fishery Management Council are working to rebuild most overfished species and have stabilized others, many in the scientific and fishing communities wonder how long those fisheries will hold up with fishing pressure increasing and the productivity of estuaries in such sharp decline.

Anglers identify the IRL with a handful of major gamefish species — snook, tarpon, spotted seatrout, and red drum. But major federally managed reef species depend on these sheltered waters as a nursery. These include a wide variety of snappers, including mutton, gray (mangrove), yellowtail, cubera, and lane snapper, plus black grouper, gag grouper, and black seabass, among others. The economic importance of these species cannot be overstated; yet the viability of these fisheries, no matter how well managed, are threatened by the continuing degradation of the estuaries that support them.

What’s happening inshore may be a harbinger of what’s to come out in the South Atlantic. There’s a consensus among the veteran inshore guides here that we’re already seeing declines in the state-managed species that rarely, if ever, leave inshore waters. Though an occasional “banner day” gives me hope, such days are fewer and farther between, which makes me question whether Florida’s statewide size and bag limits, though science-based and largely on the conservative side, are conservative enough for the declining IRL. Besides the ecological damage, recreational fishing pressure increases in step with population growth, and there are recent shifts and increases in commercial effort — particularly for spotted seatrout and pompano — on the IRL.

Let’s talk about trout. As one important ecosystem restoration document points out,

A few years ago, the Florida Fish & Wildlife Research Institute conducted a stock assessment on trout, and found that the population was exceeding its target goal of a 40 percent spawning potential ratio. That means leaving 40 percent of spawning-age fish in the water to reproduce, with a one-fish limit on trout over 20 inches to help make sure that there are plenty of larger breeding females and plump eggs to fertilize. At the urging of then FWC Commissioner Kathy Barco, the other commissioners agreed to increasing the commercial harvest and doing away with a two-month recreational closed season. Ms. Barco said she wanted “to give something back to the fishermen,” which however well intended probably wasn’t the best thing for us on Florida’s Treasure and Space coasts.

Ecological concerns notwithstanding, the increase in harvest fell within the letter of good single-species fisheries management – if there is such a thing. The trout population stood above target levels. But the commission didn’t consider the folly in assuming that the trophy trout Mecca that is the Indian River Lagoon would continue to generate strong year classes, as the very habitats, salinity levels, and forage base the young fish need to survive disappear. We are witness to increased effort by small-boat commercial hook-and-liners and more recreational boats on the water targeting trout. Many of my fellow anglers have voluntarily quit killing trout. The word is out — trout numbers are down. We all think that an IRL-specific stock assessment on trout and other important indicator species is needed. We expect that such research will confirm what we’re experiencing, and that will not be good news for other fisheries that depend upon healthy estuaries, whether they’re prosecuted in state or federal waters.

If we want to maintain healthy fisheries inshore and offshore, and legitimately maintain our claim as the Fishing Capital of the World, the destruction of Florida’s estuaries must be reversed. Until then, it is unwise to increase limits based on single-species stock assessments on estuarine-dependent species that fail to adequately consider all relevant available ecological information. It would be shear folly to weaken state or federal laws that protect essential fish habitat and guard against overfishing. We need to shift fisheries management toward ecosystem-based approaches, and demand that state and federal governments fund the restoration projects and fisheries research needed to get the job done right.