Geothermal systems can provide significant amounts of hydrothermal sulfur to surface waters, increasing salinity and avoiding some of the common anthropic uses. The objective of this study was to investigate the sedimentary neoformation of S-bearing phases in organic matter-rich sediments from a saline lake with hydrothermal inputs (Sochagota Lake, Colombia). Detrital kaolinite and quartz are the main minerals of the materials deposited in the Sochagota Lake. Neoformed clay minerals (illite and illite-dioctahedral vermiculite mixed layers) are concentrated in the central and northern part of the lake in sediments with high organic matter content. The most organic matter-rich materials are characterized by S-bearing minerals: mackinawite, pyrite, and elemental sulfur (S°). FESEM, high-resolution transmission electron microscopy (HRTEM), EDS, and Raman microspectrometry have revealed the presence of cell-shape aggregates of mackinawite nanoparticles filling the inner part of plant fragments, indicating that microorganisms were involved in the hydrothermal sulfur uptake. The alteration of mackinawite in free sulfide excess environment produced the formation of framboidal pyrite. The evolution to conditions with the presence of oxygen favored the formation of complex S° morphologies.