Investigating the mechanisms behind the impact of heavy metal pollution on aquatic ecosystems is urgently required. Due to increasing growth in the mining sector, pollution has become a serious threat to water resources and aquatic biodiversity and is causing unfavorable environmental changes and human health hazards. The aim of the present study was to investigate and assess the environmental risks of heavy metal pollution of river ecosystems in the Lake Sevan and Debed River catchment basins in Armenia, and a thorough study of their qualitative and quantitative parameters. Water samples were taken from the risky river sites of the Sevan and Debed basins in May and August 2013 and 2014. Investigations showed that due to mining and metallurgical industrial activities and the insufficient management of industrial waste and wastewater, the river ecosystems in these territories were exposed to heavy metal pollution, the degree of which in some sites of the Sotq, Masrik (Lake Sevan catchment basin), Debed, Alaverdi, Akhtala, and Chochkan (Debed River catchment basin) rivers may have posed health risks to aquatic life as well as to humans (at least in the case of river water used for drinking purposes). The results of a phytoplankton community study revealed that a decrease in the species diversity of planktonic algae in the investigated rivers was mainly conditioned by the impact of heavy metal pollution induced by mining and metallurgical industrial activities in the Lake Sevan and Debed River catchment basins.