Sulfate-reducing bacteria (SRB) and methanogenic archaea (MA) share common niches in coastal sediments during the terminal phases of the anaerobic mineralization of organic matter. The purpose of this study was to analyse the spatial-temporal variation of SRB and MA in the sediments of a tropical coastal lagoon with ephemeral inlet and its relationship with environmental changes. Sediment samples were collected during the dry, rainy and northers seasons. Microbiological analyses included the quantification of the viable SRB and MA with different substrates, as well as mineralization experiments to determine the effect of sulfate on acetate oxidation. The analyzed environmental variables included temperature, pH, Eh, salinity, sulfates, H2S, volatile solids, carbohydrates, and granulometric characteristics. Major changes occurred between the dry and rainy seasons. During the dry season, sulfate-reducing abundance was significantly greater with lactate (8.3x105-1.2x107 cells/g) and propionate (1.8x105-6.6x106 cells/g) as substrates, while the MA that use methanol were dominant (4.2x105-9.1x106 cells/g). In contrast, during the rainy season, hydrogenophylic (2.6x105-8.3x106 cells/g) and acetoclastic (5.4x105-6.4x106 cells/g) MA increased significantly and SRB decreased in the analyzed substrates. An apparent competition for acetate was observed, with a greater oxidation in the media with sulfates in the dry (0.06 mM acetate/g sediment/day) season, and a greater oxidation in the media without sulfates in the rainy season (0.02 mM acetate/g sediment/day). SRB and MA were present throughout the sediment column, however SRB dominated in the first centimeters of the sediment while MA were abundant in deeper layers. Salinity, sulfate, the organic fractions, and silt were the environmental variables that explained the SRB and MA dynamics.