The aim of the study was to compare bacterial composition and load in waters and fish related to the wastewater treatment plant (WWTP), particularly waters and wild fish affected by sugarplant processing (sugar cane and sugar beet). Aeromonads were the most frequently isolated group from water and fish. A. hydrophila was a prevailing species in isolates from water, followed by A. veronii, Rheinheimera soli and Ochrobactrum anthropi. Of indicator bacteria for aquatic contamination from fish tissues, the most prominent were V. cholerae, Enterobacter cloacae and E. sakazakii. Sugar cane processing contributed to high viable cell counts at 37 °C while sugar beet processing contributed to high bacterial counts at 22 °C. Heterotrophs from gills of effluent fish were highest during sugar cane processing. Counts retrieved from fish skin were more uniform between effluent fish and fish from downstream waters. Antimicrobial resistance of bacteria isolated from water was high against amoxicillin, sulfamethoxazole, flumequine, norfloxacin and oxolinic acid in samples from the inflow of raw municipal wastewaters to WWTP, while resistance found in bacteria from the inflow of sugarplant mostly related to sulfamethoxazole and amoxicillin. The PCA analysis associated the occurrence of high heterotroph counts, P. aeruginosa, and intestinal enterococci on skin and gills with sugar cane, and yeasts and molds with sugar beet processing. Fish living in treated wastewaters and related water bodies could pose a microbial hazard if fished for human consumption, possibly causing infection when being handled and processed, as a risk of human pathogens penetrating fish tissues. Display omitted •We evaluated microbiological impact of sugarplant effluent on wild fish.•Ubiquitous and pathogenic bacteria were retrieved from tissues; mostly aeromonads.•63% of fish aeromonads showed resistance against tested antimicrobials.•Gill and kidney histopathology showed an increased number of bacterial cells.•Multivariate tools correlated effectively microbiological data, tissues and seasons.