Algae and aquatic plants require the major nutrients-carbon, nitrogen, and phosphorus. If one of these nutrients is present in a lower proportion, it may limit the algae or plant growth. Liebig's Law of the Minimum states the growth of a plant is limited by the material in least supply. Because carbon dioxide is plentiful in the atmosphere and in water, carbon seldom is limiting to aquatic productivity. Nitrogen gas is also abundant in the atmosphere, and many blue-green algae are nitrogen fixers, meaning they can convert nitrogen gas into the organic nitrogen in cellular use.

Phosphorus has no gaseous phase. Although it is found in phosphate rocks, fertilizers, human and animal waste, and organic material, and is required in a relatively small proportion by aquatic plants, phosphorus is most often the limiting nutrient in fresh-water systems. The limiting role of phosphorus does not necessarily mean it is in scarce supply. Rather, it refers to the importance of phosphorus in regulating aquatic production. The addition of phosphorus to a phosphorus-limited lake system results in additional algae and plant growth. For this reason and because phosphorus has no gaseous phase, phosphorus is most often the target of lake management addressing excessive enrichment and plant growth.

Aquatic organisms also influence lake chemistry. Phytoplankton extract nutrients from the water and zooplankton feed on phytoplankton. Nutrients are redistributed from the upper water to the lake bottom as the dead plankton gradually sink to lower depths and decompose.

In contrast to dissolved oxygen, essential nutrients such as the bioavailable forms of phosphorus and nitrogen typically increase in the spring runoff and from the mixing of nutrients from the bottom during spring turn-over. Concentrations decrease in the epilimnion during the summer stratification as nutrients are taken up by algae and eventually transported to the hypolimnion when the algae die and settle out. During this period, any new input of nutients into the upper water may trigger a bloom of algae. Such inputs may be from upstream tributaries after storms, from die-offs of aquatic plants, from pulses of urban stormwater, direct runoff of lawn fertilizer, or from high winds that mix a portion of the nutrient-enriched upper waters of the hypolimnion into the epilimnion.