The limnology of the GSL, and its subsequent effect on birds using the system, is in large part a consequence of physical and chemical conditions. Many of the current physical features of the lake that pose major influences upon lake biology are human- produced. Among these are trans-lake causeways, solar pond impoundments for mineral extraction, and the dikes, levees, roadways, and impoundments constructed for wildlife habitat management. Each of the three major river deltas, as well as other significant wetland complexes, have been modified significantly through water diversion, distribution, and impoundment. The GSL offers a unique relationship between fresh and salt water habitats that is particularly attractive to birds. In some areas this relationship is compromised through development and in others it is enhanced. This salt water/fresh water interface is often allied with the GSL shoreline. The degree of salt and fresh water association is mostly dependant on lake elevation. At any one point in time, parts of the GSL can be removed from fresh water by hundreds of meters of exposed mud or sand bars, while at other elevations, salt and fresh water may be continually mixing along the lake. Additionally, flooding by the GSL during periods of high water elevation can cause salt water intrusion into fresh water impoundments.

Lake volume and elevation affect brine concentrations. In recent years brine concentrations are also a product of intra-lake diking. These dikes, in conjunction with lake volume, have essentially created four distinct limnological units. Each of these lake units harbors its own halophyte and halophile community. Some of these lake complexes are important as waterbird foraging sites. These conditions within the Great Salt Lake Ecosystem provide for diverse habitat conditions that are dynamic through climatic cycles. There are four and one half billion tons of salt in the GSL system, distributed throughout the lake in solution or as bottom precipitants.

There is also an important relationship between shoreline conditions and brine fly production. When brines exceed 60 ppt (parts per thousand) at the shoreline and there is an appropriate substrate, profound populations of brine flies are produced in the warm seasons. Thousands of brine fly adults can occur per square meter. A recent survey of brine fly pupae casings estimated nine billion casings washed up on shore along a six-mile stretch of the Antelope Island State Park Causeway (Paul et al. 2001c). Hundreds of waterbirds may be found when these brine conditions and associated brine fly populations are located in close proximity with the distinct emergent vegetation and abundant macroinvertebrate populations of fresh water wetlands or drainages.