The forms of sulfur available in aquatic environments depends on whether it is a marine or freshwater environment. Freshwater environments are more varied and subject to a multitude of sulfur inputs and outputs, including atmospheric deposition, runoff, diagenesis of bedrock and the presence of microbial sulfate reducers (MSR). Overall, the main species of sulfur in freshwater environments are hydrogen sulfide and sulfate. In estuaries, plant roots extend into sulfide-rich, S-depleted sediments created by MSR, and incorporate that sulfide into their biomass. However, levels of sulfide produced by MSR can be toxic, and it has been proposed that these plants pump oxygen into their roots to oxidize sulfide into the less toxic sulfate. In these environments algae will preferentially acquire sulfur from HS if present, rather than the more abundant sulfate, as sulfide can be readily incorporated into the direct formation of cysteine. This is consistent with cyanobacteria being able to carry out anoxygenic photosynthesis using sulfide.
In marine environments, the main forms of sulfur available is in sulfate at ~29 mM and a δS of 21‰ in seawater. At the surface of the sea, this excess in sulfur is subsequently converted into dimethylsulfoniopropionate (DMSP) by algae as an osmolyte and a repellent against grazing. DMSP also accounts for 50–100% of bacterial sulfur demand, making it the most important source of reduced sulfur for marine bacteria. DMSP's cleavage product dimethyl sulfide (DMS) is highly volatile, escaping the ocean into the atmosphere with emissions ranging between 15 and 33 Tg S year  and accounting for 50–60% of the total natural reduced sulfur flux to the atmosphere. In seafloor sediments, microbial sulfate reduction is a major biogeochemical process that consumes organic carbon. Microbial sulfate reduction can completely use up sulfate from the seawater and accumulate hydrogen sulfide in the sediment. Sulfide reoxidation and disproportionation are also thought to be major processes affecting the sulfur isotopic compositions of marine minerals and sediment porewater.