Production of antibiotics and enzymes by microorganisms is well recognized for its economic benefits. Searching potentially exploitable microorganisms, strains of heterotrophic bacteria were isolated from marine and estuarine waters in Niterói-RJ, Brazil, and tested for the production of enzymes and antimicrobial substances. From the 76 isolated colonies, 09.21% showed antimicrobial potential, 63.16% showed enzymatic activity for at least one of the substrates tested and 91% showed multidrug resistance. Strains that presented the better results were identified by sequencing. The species identified are widely distributed in many different types of environments, having been isolated previously from marine environment. Our results suggest that marine and estuarine waters can be a source for bioprospecting bacteria with potential biotechnological uses.