Molecular DNA techniques have established that distinct differences occur in the phylogenetic make up of microbial populations in freshwater and marine ecosystems (Nold and Zwart 1998; Crump et al . 1999). Recently it was also shown that shifts in microbial composition occur along fresh to brackish gradients in riverine/estuarine systems (Bouvier and del Giorgio 2002). Metabolic activities of planktonic bacteria also are known to vary in space and time along a riverine/ estuary gradient (Schultz and Ducklow 2000; del Giorgio and Bouvier 2002). In the latter study, salinity was an important determinant in separating bacterial communities