The present field investigation considers monitoring some biotic (four fish species and plankton) and abiotic (water and sediment) components as indicators of natural and anthropogenic impacts on aquatic ecosystem during winter and summer seasons. This included measurement of metal concentrations in water, sediment and plankton samples, conducting a risk assessment of sediment pollution and evaluating fish body condition indices as well as oxidative stress biomarkers. The detected seasonal variation among these parameters showed site-related and species-specific patterns. The levels of metal in plankton samples were, in most cases, higher than those in sediment samples and the lowest levels were detected in water samples. Heavy metal enrichment status in sediment showed mostly a progressive pollution condition during summer as well as seasonal fluctuation in levels of Zn and Pb along the studied sites. The scaled mass index (SMI), as a fish body mass-length index, performed better in indicating the fish body condition in relation to the ecosystem condition, where it showed significant increase in case of the flathead mullet (Mugil cephalus) and the green tilapia (Tilapia zillii) during summer and significant increase in the Nile tilapia (Oreochromis niloticus) and the catfish (Clarias gariepinus) during winter. Mullet showed the highest levels of oxidative stress biomarkers (superoxide dismutase, catalase and malondialdehyde), while Nile tilapia showed the lowest levels. The present study affirms the significance of monitoring sediment geoaccumulation index (Igeo) and pollution load index (PLI) as well as SMI and oxidative stress biomarkers as sensitive indicators of intricate pollution conditions and their effects on aquatic ecosystems.