Biogeochemistry is the science of processes that control the chemical structure and composition of the natural environment in the Earth’s surface reservoirs and also the transport rates of matter between them.

The Earth system reservoirs in question are: the biosphere, the hydrosphere (oceans, lakes, rivers, ground water), the atmosphere, the pedosphere (soils), the cryosphere (ice on land and on the ocean), and the surface of the lithosphere (sediments, different rock types).

Biogeochemistry deals in particular with the cycles of elements which involve the interaction with biota, such as the cycles of carbon, oxygen, nitrogen, and phosphorus. Biogeochemistry is a part of the larger overall discipline geochemistry.