Streams and rivers are among the most vulnerable water resources to contamination due to their extensive contact with terrestrial environments. Contaminated streams and rivers pose significant threats to downstream ecosystems. This study examined water quality parameters in lotic or potamic habitats (n = 60) that flow into the Marmara Sea. Samples were collected during the spring season (May 12–26, 2024) and analysed for ten limnological parameters, including dissolved oxygen (DO), electrical conductivity (EC), pH, total dissolved solids (TDS), nitrate nitrogen (NO3–N), nitrite nitrogen (NO2–N), ammonium nitrogen (NH4–N), phosphate phosphorus (PO4–P), turbidity, and salinity. The average values of these parameters were 6.76 mg/L for DO, 4.00 NTU for turbidity, 1.23 mg/L for NO3–N, 0.20 mg/L for NO2–N, 0.91 mg/L for NH4–N, and 0.35 mg/L for PO4–P. Water quality was further examined using statistical and ecotoxicological indicators to assess potential risks to ecosystems and human health, including concerns related to mucilage formation. This study employed a range of statistical models—including principal component analysis (PCA), cluster analysis (CA), water quality index (WQI), nutrient pollution index (NPI), hazard quotient (HQ), hazard index (HI), and geospatial mapping—to deliver a comprehensive toxicological, statistical, and spatial assessment. The results identified the Gemlik and İzmit Gulfs as the highest-risk zones for the Marmara Sea. Additionally, high population densities, industrial activities, and inadequate infrastructure in the watersheds of the Gemlik, Gebze, Şerefli, and Çanakkale streams were identified as significant stressors for the Marmara Sea ecosystem.
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