This study investigates the anthropogenic activities, water quality, and ichthyofaunal diversity of the Navotas Riverine Ecosystem. It examines the anthropogenic influences, analyzes the physicochemical and microbiological properties of water, identifies fish species, evaluates the water quality index, and determines ichthyofaunal diversity using various indices. Water samples and fish collections were conducted from January to April 2024 at three sites. Key findings indicate that water quality parameters such as temperature (23.20-37.5°C), dissolved oxygen (6.22-7.84 mg/L), phosphate concentration (0.55-3.72 mg/L), and fecal coliform (350-160,000 MPN/100 mL) failed to meet DENR standards for Class C water. The TDS (1153.33-10700 ppm) and conductivity (17653.33-21333.33 µS/cm) were also elevated, indicating significant pollution. The study identified low ichthyofaunal diversity, with six native and one invasive fish species. A total of 269 fish were collected: 161 from Site 1, 46 from Site 2, and 62 from Site 3. The most abundant species was Scatophagus argus (19% occurrence), while the invasive Sarotherodon melanotheron ranked third (17% occurrence). Notably, pH (r = 0.753) correlated highly with nitrate concentration. S. melanotheron significantly correlated with pH (r = 0.602, p = 0.019) and nitrates (r = 0.555, p = 0.031). Lutjanus argentimaculatus also had significant correlations with pH (r = 0.527, p = 0.039) and nitrates (r = 0.651, p = 0.011). Conversely, S. argus had a negative moderate correlation with temperature (r = -0.529, p = 0.039) and conductivity (r = -0.536, p = 0.036). These correlations suggest that the water parameters significantly influence the diversity and abundance of fish in the river. The study concludes that the river's water quality is heavily influenced by anthropogenic activities which negatively affect ichthyofaunal diversity. Recommendations include continuous monitoring, gut and heavy metal analysis of fish, assessment of avifauna diversity, and strict implementation of conservation regulations.