In a joint Brazilian-German case study, distribution patterns of microorganisms were compared with environmental variables in the tropical coastal Manguaba lagoon in northeast Brazil, which is situated downstream of several sugar cane processing plants . 16S rDNA and 16S rRNA single strand conformation polymorphism (SSCP) gene fingerprinting were used to follow the composition and distribution of microorganisms throughout the salinity gradient of the lagoon. Potentially abundant microorganisms were identified by sequencing representative SSCP bands. It could be demonstrated that the distribution of microbes was in close relation to the physico-chemical environmental settings and followed a common scheme. In the in- and outlet areas of the lagoon rather transient microbial communities were found, whereas in the central part a stable, diverse community was encountered, that due to the long residence time of the water, had ample time for development and adaptation.