In the absence of any living organisms, a lake contains a wide array of molecules and ions from the weathering of soils in the watershed, the atmosphere, and the lake bottom. Therefore, the chemical composition of a lake is fundamentally a function of its climate (which affects its hydrology) and its basin geology. Each lake has an ion balance of the three major anions and four major cations (see Table 4).

Table 4. ION BALANCE FOR TYPICAL FRESH WATER
Anions	Percent	Cations	Percent
HCO3-	73%	Ca+2	63%
SO4-2	16%	Mg+2	17%
Cl-	10%	Na+	15%
		K+	4%
other	< 1%	other	< 1%

Ion balance means the sum of the negative ions equals the sum of the positive cations when expressed as equivalents. These ions are usually present at concentrations expressed as mg/L (parts per million, or ppm) whereas other ions such as the nutrients phosphate, nitrate, and ammonium are present at µg/L (parts per billion, or ppb) levels.

Humans can have profound influences on lake chemistry. Excessive landscape disturbance causes higher rates of leaching and erosion by removing vegetative cover, exposing soil, and increasing water runoff velocity. Lawn fertilizers, wastewater and urban stormwater inputs all add micronutrients such as nitrogen and phosphorus, major ions such as chloride and potassium, and, in the case of highway and parking lot runoff, oils and heavy metals. Emissions from motorized vehicles, fossil fuel-burning electric utilities and industry, and other sources produce a variety of compounds that affect lake chemistry.

Perhaps the best understood ions are H⁺ (hydrogen ion, which indicates acidity), SO₄^-2 (sulfate) and NO₃^- (nitrate) which are associated with acid rains. Mercury (Hg) is another significant air pollutant affecting aquatic ecosystems and can bioaccumulate in aquatic food webs, contaminating fish and causing a threat to human and wildlife health (see also the Minnesota Pollution Control Agency’s section on Hg).

Lakes with high concentrations of the ions calcium (Ca⁺²) and magnesium (Mg⁺²) are called hardwater lakes, while those with low concentrations of these ions are called softwater lakes. Concentrations of other ions, especially bicarbonate, are highly correlated with the concentrations of the hardness ions, especially Ca⁺². The ionic concentrations influence the lake's ability to assimilate pollutants and maintain nutrients in solution. For example, calcium carbonate (CaCO₃) in the form known as marl can precipitate phosphate from the water and thereby remove this important nutrient from the water.

The total amount of ions in the water is called the TDS (total dissolved salt, or total dissolved solids concentration). Both the concentration of TDS and the relative amounts or ratios of different ions influence the species of organisms that can best survive in the lake, in addition to affecting many important chemical reactions that occur in the water. One example of particular interest in the Great Lakes region involves the calcium requirement of the exotic zebra mussel that is causing profound changes in Lake Erie (see National Aquatic Nuisance Species Clearinghouse or Sea Grant Nonindigenous Species Site). Lake Superior appears to be relatively immune to infestation by this invader because of low calcium concentration. Its bays, however, such as the lower St. Louis River and Duluth-Superior Harbor, may not be immune to zebra mussel infestation.