Heavy metal and aluminum pollution of the hydroecosystems in the catchment areas of the Voghchi and Meghriget rivers and risks to the environment associated with water pollution were investigated. The catchment areas of the Voghchi and Meghriget rivers are situated in the south of the Republic of Armenia where mining and metallurgical industries are highly developed. The investigations revealed that the Voghchi, Geghi, Artsvanik and Meghriget rivers were polluted with heavy metals and aluminum. Comparatively high concentrations of heavy metals and aluminum in the studied rivers were registered after Qajaran, Kapan and Meghri towns and the tailings storage facility of Artsvanik which may have been conditioned by the influence of wastewaters from urban mining and metallurgical and domestic activities. The assessment of changes in the species composition of phytoplankton community performed by the Menhinick diversity index revealed that ecosystem conditions were deteriorated in the Voghchi river after Kapan town and the Artsvanik river after the tailings storage facility which may have been conditioned by heavy metal and aluminum pollution.