The three major harbours from the central west coast of India were investigated for their benthic environmental status using nematodes as surrogate community. As these three harbours have shown deteriorated conditions revealed from macrobenthic community, our main objective was to investigate and inter-compare the nematode communities within these harbours and with other similar habitats worldwide. A total of 50 nematode species was encountered in the study area, wherein highest (34 species) were recorded at Mormugao harbour and lowest (23 species) at Ratnagiri harbour. The presence of dominant species like Vasostoma sp. (41%), Sabatieria sp. 1 (23%) and Sabatieria sp. 2 (20%) designate these harbours as altered benthic habitats under stress. The diversity indices demonstrate Ratnagiri harbour as the most stressed and Karwar being the least stressed comparatively. Intense anthropogenic activities, input of many pollutants such as heavy metals, pesticides, petroleum derivatives, TBT’s and dredging activity in the harbours can be held responsible for the altered nematode community