The data comprises all standard water quality parameters (including chemical oxygen demand, pH, dissolved oxygen, total dissolved solids), viable counts of heterotrophic bacteria and resistant bacteria and Escherichia coli, qPCR measured concentrations of 7 antibiotic resistance genes, 1 mobile genetic element gene, an E. coli specific gene and 16S rDNA. Samples were taken from the Musi river, upstream, within the city of Hyderabad, India, and downstream of the city, during the wet season of 2022 and the dry season of 2023. The Musi catchment is both rural and urban, including many residential communities, hospitals and factories. Downstream of the city, land use includes agriculture and aquaculture, with less human impact than within the city stretch. Sampling sites were chosen to contrast upstream water conditions with sites in the city and downstream. Both water and sediment grab samples were collected by a team from the Indian Institute of Technology Hyderabad. The data was collected to study the sources and fate of pollution with antimicrobial resistance. Full details about this dataset can be found at https://doi.org/10.5285/42e992f7-67b1-44dd-90de-f5990269b00e