Continuous monitoring of the water quality in Canton Sarajevo is one of the top priorities necessary for water management, pollution control and conservation efforts in the region. This study presents a comprehensive assessment of water quality in the interconnected river systems of Miljacka and Zeljeznica, employing a multianalytical approach. Water and fish samples were collected at three sites and analysed for the presence of microorganisms, heavy metals and organic pollutants. Physicochemical parameters were examined to understand the rivers’ overall health and ecologic condition. Histopathological analysis of fish species native to these two rivers served as a bioindicator of environmental stressors. In general, there were less anthropogenic pressures found at Site 1 – Kozija ćuprija (river Miljacka – upstream from the city of Sarajevo) and 3 (river Zeljeznica – downstream from the city of Sarajevo). Site 2 – Otoka (river Miljacka, city center) had the highest concentrations of lead, ammonia, orthophosphates and BOD5, as well as total coliform bacteria. This may be linked to the runoff from sewage. The detected histopathological changes are probably associated with the combined microorganisms and organic pollutants, among which plasticizers, emulsifiers, solvents, surfactants and additives were detected by GC-MS.