Agrochemicals applied to agricultural fields, household gardens, roadsides, or any other place can get transported by spray drift, drainage, wind, rain or run-off, and eventually enter streams, ponds, lakes, and other reservoirs of natural water. In these aquatic systems, agrochemicals may be exposed to various abiotic physical processes and biotic agents living under aerobic or anaerobic environments. The aerobic and anaerobic aquatic metabolism studies are conducted to measure the rate of degradation of the agrochemical test substance, identify its transformation products and determine their rates of formation and decline in water–sediment systems. The tests are carried out using either flow-through systems or biometers. This chapter discusses the procedures to be followed to collect water and associated sediment, set up the experiment and analyze samples under regulatory guidelines while conducting these aquatic metabolism studies. The degradation rate and half-life (DT50) of the agrochemical under aquatic environment are determined using first order kinetics and other statistical methods. The steps involved in a sample anaerobic aquatic metabolism study are described with examples. Metabolic pathways of a selected group of agrochemicals in aerobic and anaerobic aquatic conditions are also discussed in the chapter.