Mullet (Mugil liza) were sampled in five different areas along the Guanabara Bay, southeastern Brazil, classified as non-contaminated, moderately contaminated and contaminated. Morphometric (Fulton condition factor, relative condition factor and weight to length scaling coefficient) and organosomatic (hepatosomatic index) indices of environmental stress were analysed. Fish from the differentially contaminated areas show statistically different Fulton and relative condition factors and hepatosomatic indices, but not the weight to length scaling coefficient. The Kn and the FCF followed the same trend, with fish from São Gonçalo (1.07 ± 0.04 and 0.89 ± 0.03), Itaipu (0.84 ± 0.01 and 0.86 ± 0.01) and the Rodrigo de Freitas Lagoon (1.03 ± 0.01 and 0.87 ± 0.20) showing higher FCFs than fish from Magé (0.96 ± 0.01 and 0.81 ± 0.01). Fish from Itaipu showed significantly higher HSI values than the other sampling sites (1.68 ± 0.07), with fish from Olaria and Ipiranga showing the lowest (1.56 ± 0.12 and 1.60 ± 0.07, respectively).