Water samples were collected from three sites (Ogbakiri, Choba and Iwofe) of the New Calabar River and were evaluated for microbiological and physico-chemical characteristics. Bacterial isolates consisting mainly of gram-negative bacteria (Escherichia coli, Proteus vulgaris, Acinetobacter spp, Pseudomonas aeruginosa, Enterobacter aerogenes, Klebsiella spp., Vibrio sp. and Nocardia asteroides) were isolated from the samples. The highest total coliform counts log10 2.9 were encountered in water samples from Iwofe but the lowest counts log101.9 occurred in the water samples from Ogbakiri. Ecological parameters varied among the sites with the highest pH value of 7.87 occurring at Iwofe and lowest of 6.12 at Choba. Maximum salinity level of 150/00 was observed at Iwofe and lowest at Choba. In contrast, maximum dissolved oxygen of 10.1ppm was observed at Choba and the minimum at Iwofe. The different bacterial profiles are probably attributable to the anthropogenic and industrial activities of the sites.