Endemic to the lake are the endangered June sucker and the Utah Lake sculpin, now extinct. Although 13 species of fish are native to the lake, only the June sucker and Utah sucker remain, together constituting less than one percent of the biomass. By far the dominant species in the lake is the common carp, introduced in 1881 as an alternative to the overharvested native fish. Common carp are now estimated at 90.9% of the biomass, contributing to a decline in native fish populations by severely altering the ecosystem.
Despite its large surface area, the lake is shallow; it has a maximum depth of 14 feet (4.27 m) and an average depth of about 9.4 feet (2.74 m). This shallowness allows winds to easily stir up sediments from the lake's bottom, contributing to the turbidity seen in Utah Lake's water.
Utah Lake's wetlands are an important stopover and nesting area for migratory birds. More than 220 species of birds use these wetland areas. Utah Lake Wetland Preserve is located at the south end of the lake, in and around Goshen Bay.
The rapidly growing population of Utah Valley threatens the future of Utah Lake. Various proposals to dike the lake's bays occasionally surface. Recent development along the lake's western shore has fueled a proposal to construct a causeway across the lake. To date, economic costs, environmental concerns, litigation, and public opposition have stymied these proposals.
Historically, Bonneville cutthroat trout were the predator fish in the ecosystem, and were present in large numbers; in 1864, a commercial fisherman hauled in a single net holding between 3,500 and 3,700 pounds (1,588-1,678 kg) of trout. By 1874, laws were in place to protect Bonneville cutthroats, but commercial netting was not banned until 1897. The trout population in Utah Lake was extinct by the 1920s. Today, the primary predators in the lake are the non-native walleye and white bass.
As of 2006, fishing regulations for Utah Lake released by the Utah Division of Wildlife Resources protect certain large-bodied nonnative predator species in the lake, such as bass and walleye; anglers are required to release largemouth and smallmouth bass over in length, and can take only one walleye over . In an effort to control the population of white bass and walleye, the DWR places no limit on the number of white bass that can be taken, a limit of six fish on walleye (one over 20 inches), and requests anglers to harvest them from the lake.
The June sucker (Chasmistes liorus) lives naturally only in Utah Lake and the Provo River. The species was federally listed as endangered April 30, 1986. The June sucker is unique among the sucker family of fish in that it is not a bottom-feeder, but has evolved a mouth that allows it to collect zooplankton from the water. June suckers are dark gray or brownish dorsally, with a white or slightly greenish belly. They can reach a weight of 5 pounds and have a long life span of over 40 years.
June sucker were once abundant in Utah Lake, but several factors have brought the species to the brink of extinction. Some contributions to its decline include predation on its young by introduced species such as the white bass and walleye, overfishing, pollution and resulting turbidity in Utah Lake, drought, alteration of water flow, and the introduction of carp, which eat native vegetation and various floaties that provide shelter and food for June sucker.
Biologists have been rearing the June sucker in Red Butte Reservoir and releasing them into Utah Lake to help build the population. During the summer of 2005, over 8,000 June sucker were released into Utah Lake.
The Utah Lake sculpin (Cottus echinatus) was a species of freshwater sculpin endemic to Utah Lake. The species is believed to have disappeared during the 1930s, when a severe drought led to a rapid fall in water levels in the lake. A cold winter led to the lake freezing, resulting in the overcrowding of the remaining fish. This, along with decreased water quality from agricultural practices has been identified as the likely cause of extinction.
Introduced to the lake in 1881 as a source of food after native species had been depleted by overfishing, the common carp has become the dominant species in the lake and has perhaps had the most detrimental effect on the lake's ecosystem.
Carp are estimated to make up 91% of the lake's biomass, with an adult population numbering around 7.5 million. The average carp in the lake is about 5.3 pounds (2.4 kg), for a total of nearly 40 million pounds (18 143 695 kg) of carp in the lake.
Due to their habit of grubbing through bottom sediments for food, carp stir up sediments and increase the turbidity of the water. In addition, they destroy submerged vegetation that holds sediments in place and provides shelter for native fish populations. Without vegetation, winds can more easily stir up sediment from the bottom of the lake (already a problem due to the lake's shallowness), resulting in greater turbidity and less sunlight reaching the remaining vegetation. Without cover for their young, native fish such as the June sucker become easy prey for white bass, walleye, carp, and predators.
Because carp have had such an effect on the June sucker, a large part of the work done by the JSRIP is studying means of removing or reducing the carp population. The program is still studying viable methods of removing carp, such as selling them as animal feed or possibly poisoning the lake. It is hoped that removal of carp and other invasive species will restore the lake to something resembling its natural state, providing a better environment for the June sucker and other native species such as the once-abundant Bonneville cutthroat trout.
The fish were being tested as part of the JSRIP's efforts to reduce and control the carp population and determine if they are safe for human or animal use. Of all the chemicals tested, which included mercury, only PCBs were found in elevated levels.
Because elevated levels of PCBs were found in carp, it is feared that other fish species in the lake may also be contaminated. This summer other types of fish will be collected and analyzed. According to the advisory, "an environmental investigation will be initiated as an effort to track down and clean up the source of PCBs, if possible."
The lake was more popular historically, before declining water quality made it less attractive for recreational use. Amusement resorts operated in the late 19th and early 20th centuries at Saratoga Hot Springs in the northwest corner of the lake, and at Geneva in the northeast. Geneva (named after the owner's daughter, not the lakeside city in Switzerland) was built where the Lindon Marina is now, at the point the railroad came closest to the lake. It included a hotel, swimming pools, a dance floor, and water slides. It lent its name to nearby Geneva Steel.