In 1916, the
St. Lucie Canal (C-44) diverts excess nutrient-rich water from
Lake Okeechobee into the South Lagoon. While this helps prevent life-threatening flooding in the Okeechobee area, it creates toxic blooms after entering the Lagoon, a threat to flora, fauna, and humans. This situation is proving difficult to address in the 21st century.
Mangroves are important to marine life. Between the 1940s and 2013, 85% of them had been removed for housing development. In 1990, the
Florida Legislature passed the Indian River Lagoon Act, requiring most sewer plants to stop discharging into the lagoon by 1996. Some sports fish rebounded in population in the 1990s when
gill nets were banned and pollution in the lagoon was reduced. In 1995 the seagrass covered over . The 1993–1996 data base used to track the movement of water through the St. Lucie Estuary and into Indian River Lagoon is described in Smith (2007). This includes daily mean discharge rates for the 16 gauged canals emptying into the St. Lucie Estuary and Indian River Lagoon, predicted shelf tides, and wind speeds and directions recorded along the west side of the lagoon at about 27°32'N (corresponding to Segment 11 of the model). In 2007, concerns were raised about the future of the lagoon system, especially in the southern half where frequent freshwater discharges seriously threatened water quality, decreasing the salinity needed by many fish species, and have contributed to large
algae blooms promoted by water saturated with plant fertilizers. In the mid 1990s, the lagoon has been the subject of research on light penetration for
photosynthesis in
submerged aquatic vegetation. In 2010, of nitrogen and of phosphorus entered the lagoon. In 2011, a
superbloom of
phytoplankton resulted in the loss of of lagoon seagrass. In 2012, a brown tide bloom fouled the northern lagoon. The county has approval for funds to investigate these unusual blooms to see if they can be prevented. Catches of
blue crabs dropped unevenly from in 1987 to in 2012, but with high catches in 1998, 1991, alternating with low catch years. These crabs require 2% salt content in the water to survive. A drought increases the salt content and heavy rainfall decreases it. Both of these conditions have recurred over the past decades and are believed to have had an adverse effect on the crab population. In 2013, algae blooms and loss of sea grass destroyed all gains. In 2016, there were an estimated 300,000 septic tanks in the five-county area bordering the Lagoon. At one time, sewer plants were worse polluters. In 1986, there were 46 sewer plants along the lagoon. They discharged about daily into the estuary. The state ended most sewer plant pollution by 1995. The worst fish kill to date occurred in March 2016, with 30 species impacted. A brown tide bloom, caused by the algae species
Aureoumbra lagunensis, was blamed for the low oxygen levels. The algae growth originated in the no-motor zone of the
Merritt Island National Wildlife Refuge. In 2018, lagoon health is better near ocean inlets. Pollution is worse in areas near no inlets, such as the Mosquito Lagoon, North IRL, and the Banana River. ==Economy==