The Subterranean freshwaters biome includes streams, small lakes and aquifers beneath the earth’s surface and potentially has the largest volume of water of all the freshwater biomes.

In the absence of sunlight, these ecosystems rely on allochthonous energy sourced from surface ecosystems via connected waters and in situ chemoautotrophs. Depending on the mode of connectivity to the surface, water flow-through varies from extremely rapid to slow. Highly connected subterranean streams in monsoonal climates undergo seasonal flooding and drying cycles. In contrast, paleo-aquifers are characterised by slow, low-variability seepage over millennial time scales.

Inflowing water is the principal source of dissolved oxygen and mineral nutrients, although some nutrients are liberated by in situ weathering of lithic substrates. The water regime largely determines environmental variability in subterranean freshwaters, but these systems may occasionally be influenced by mass movements.

The trophic structure of subterranean waters is typically truncated, although photosynthetically inactive algae and higher-plant propagules may be transient occupants in systems that are connected to the surface. Chemoautotrophic and heterotrophic microbes in biofilms and the water column dominate the trophic web, supporting small invertebrate detritivores and predators. Small predatory fish may occur in streams and lakes, where voids in the subsurface are of sufficient size. Productivity, metabolic rates, life histories and the diversity of the biota all reflect resource scarcity but may vary depending on water source. Insular systems exhibit high levels of endemism.