Benthic pollution assessment based on macrobenthic community structure with environmental variables was carried out at twelve stations during two periods on a presumed pollution gradient in Gamak Bay. Univariate and multivariate methods were applied to investigate structural changes in the benthic communities. A clear gradient of pollution effects on the macrobenthic community was observed from the interior to the exterior of the bay. The community on the northwestern basin was severely disturbed due to a low level of hydrodynamics and a large amount of pollutant input from nearby cities. Exterior regions on the southern basin appeared to have the best benthic environmental characteristics among all stations according to most methods of analysis. Central ridge regions and two stations around the islets in the mouth of the bay exhibited intermediate levels of perturbation when compared to the more disturbed interior and undisturbed exterior regions. Pollution effects on the communities were attenuated at the southern area of the central ridge during spring compared to those of summer, where aquacultural farming was densely distributed. The environmental variables primarily correlated to the macrobenthic community structure were total organic carbon (C), organochlorine pesticides (OCPs), and tributyltins (TBTs), contents found on the surface sediment, as anthropogenic variables indicating organic materials.