Antibiotic resistance patterns of bacterial microbiomes isolated from the New Calabar River were used to build up models on the possible effects of environmental pollutants on antibiotic resistance. The microbiomes were obtained from water and sediment samples collected at georeferenced sites on the river. This is the basis of the microbiome biogeochemico-graphic information system (MBCGIS). A combination of nutritional and physicochemical factors is presented as support for the existence of microbiome antibiograms in ecosystems challenged with environmental pollutants.High incidence of antibiotic resistance in environments with pronounced industrial and human activities, suggest possible effects of pollutants on the ecosystem. A weak correlation (r = 0.28) between incidence of antibiotic resistance and faecal coliforms implies that the antibiotic resistance patterns of microbiomes may be due to factors that are not linked to faecal pollution. The presence of chemical pollutants may contribute to the risk of increased antibiotic resistance in the environment. Sustainable development demands rigorous legislation for the protection of natural water resources.