A study was conducted to determine the prevalence, serotypes, antimicrobial resistance and plasmids profiles of Salmonella spp. in Nile perch (Lates niloticus) from Lake Victoria, Tanzania. Presence of Salmonella spp. and quantification of Escherichia coli in water and fish were investigated using standard bacteriological methods. Antimicrobial resistance was determined using minimum inhibitory concentration (MIC) method. A total of 352 samples were analysed including Nile perch, lake water and swabs from surfaces of facilities used for fish transportation. A total of 10 different Salmonella serovars were isolated. Salmonella enterica subsp. salamae with antigenic formula 42:r:- had a prevalence of 10.0% (n = 60) in Nile perch from fishing grounds which were significant different (P < 0.05) to the prevalence of this serovar at landing sites and domestic markets 1.7% (n = 60 each). The prevalence of Salmonella Waycross (41:z4, z23:-) in Nile perch from fishing grounds was 18.3% (n = 60) with no significant difference (P > 0.05) compared to the ones at landing sites 10% (n = 60) and markets 13.3% (n = 60). The prevalence of S. enterica subsp. salamae 42:r:- in water from fishing grounds was 6.7% (n = 60). Two out of 12 S. enterica subsp. salamae 42:r:- were resistant to sulfamethoxazole, while one was resistance to azithromycin. S. Waycross were resistant to sulfamethoxazole (6/30), azithromycin (6/30) and ampicillin (4/30). Seven S. Waycross carried plasmids, but none of S. enterica subsp. salamae 42:r:- carried plasmids. E. coli mean counts were 2.51 log cfu/g in fish intestines, 2.38 log cfu/g in gills, and 2.02 log cfu/ml in water. The frequent findings of S. enterica subsp. salamae 42:r:- and S. Waycross in Nile perch are surprising as these serovars are rarely associated with human diseases. Follow-up studies of their ecology in Nile perch and Lake Victoria are needed.