Lake Sevan is the second largest high-mountain lake in the Caucasus, with economic, historical and cultural significance. During the study period of 2015–2019, a total of 209 species of algae and cyanobacteria from eight taxonomic divisions were identified in the phytoplankton of Lake Sevan. Among them, diatoms increased their presence during the study period. The abundance and biomass values increased during the study period, while bloom outbreaks occurred with greater frequency. The Dolichospermum cyanobacterial species causing bloom in the summer, releasing toxins, were noted as posing a threat to the rational use of Lake Sevan. The species number in Big Sevan was generally lower than in Small Sevan. The simultaneous decrease in species richness during the study period from 2015 to 2019 from 53 to 40 species, the Shannon Index from 0.61 to 0.06 and the Saprobic Index from 2.00 to 1.73 reveals a tendency towards restructuring of the ecosystem of Lake Sevan towards simplification. In combination with an increase in quantitative indicators of phytoplankton and the number of species of eutrophic state indicators, these dynamics show an increase in the imbalance of the ecosystem. Redundance Discriminant analysis indicates an increase in water pH and copper concentration as negative factors, and an increase in the total ionic composition and temperature as factors stimulating the development of phytoplankton. Statistical maps revealed points on the coast of Lake Sevan responsible for factors influencing its ecosystem according to various variables, including copper influx. The analysis also revealed sufficient capacity of the ecosystem of Lake Sevan for self-purification during the study period. For the first time, 99 species of diatoms and cyanobacteria with IUCN categories were identified for Lake Sevan, seven of which are considered threatened. The number of threatened species of categories CR and EN decreased between 2015 and 2019, indicating adverse impacts on sensitive ecosystem species. An assessment of the changes occurring in Lake Sevan indicates the need to continue hydroecological monitoring in combination with bioindication and statistical methods and an inventory of all factors affecting the stability of the ecosystem of the high-mountain Lake Sevan.

River fragmentation is a major anthropogenic disturbance that modifies hydrological conditions, influences abiotic parameters, and thus also affects phytoplankton composition, diversity, and abundance. Mountain river ecosystems are particularly vulnerable. In the local context of Caucasus rivers, disruptions of ecological continuity are also important because the flux of untreated wastewater or the discharge of drinking-water-quality effluents affects water quality and thus biota substantially. However, the response of phytoplankton communities to river fragmentation is not well studied yet. Therefore, the present study addresses such a gap in the knowledge by investigating the phytoplankton community of the heavily fragmented Hrazdan River in the central part of Armenia and evaluating the effects on its taxonomic composition, diversity, and community structure. Comprehensive analysis involving hydrochemical, hydrophysical, and phytoplankton metrics revealed that both river fragmentation and disruption of ecological continuity have a strong influence on phytoplankton communities. Factors such as severe organic enrichment, elevated nutrient loads, and critical oxygen depletion create chemical barriers that induce additional ecological fragmentation. PCA and cluster analysis showed major patterns of impacts of the interaction between physical barriers and localized anthropogenic stressors, which drive distinct taxonomic regrouping within the phytoplankton community. Overall, this study demonstrates that phytoplankton dynamics in regulated mountain rivers are primarily governed by the coupling between chemical stressors and fragmentation-induced habitat alterations, highlighting the need to conduct river restoration at various parts.