The Lakes biome includes lentic ecosystems defined by their still waters. They vary in area, depth, water regime, and connectivity to other aquatic systems across a global distribution.

Gradients in water regimes, temperature, lake size, and salinity exert critical influences on the function, productivity, diversity, and trophic structure of lake ecosystems. Water regimes vary from permanent open waters to seasonal or episodic filling and drying on interannual time scales. Lakes span global climatic gradients, which influence their water regimes through catchment precipitation and evapotranspiration rates, as well as the seasonal freeze-thaw cycles of lake surfaces along latitudinal and altitudinal temperature gradients.

The azonal character of the Lakes biome, however, is due to the buffering of climatic influences by groundwater, geomorphology, and substrate. This is most evident in the water regimes of artesian springs, oases, and geothermal wetlands, as their water sources are largely independent of climate. Lake and catchment substrates influence nutrient stocks and salinity, but concentrations may vary temporally depending on water regimes and mixing. Deeper and freeze-thaw lakes are often characterised by stratification, producing depth gradients in nutrient and oxygen availability and temperatures. The deepest lakes extend to the aphotic zone. Productivity is determined by allochthonous inputs from the catchments and autochthonous inputs from phytoplankton, periphyton (i.e. biofilms), and submerged, floating and emergent macrophytes.

Trophic webs tend to increase in size and complexity with lake size due to increased resource availability and niche diversity, but small shallow lakes have greater diversity than small deep lakes due to habitat heterogeneity and light penetration to the bottom allowing development of benthic macrophytes and associated biota. Salt lakes may have high productivity but simple trophic structures, with high abundances of few species. Invertebrate detritivores consume fragments of organic matter, providing resources for macroinvertebrates, fish, waterbirds, reptiles, and mammals. Species traits appear to be strongly influenced by environmental filtering by the water regime (e.g. cold tolerance and seasonal dormancy occurs in freeze-thaw lakes, and desiccation tolerance and dormant life stages dominate in ephemeral lakes) and water chemistry (e.g. tolerance to salinity in salt lakes).