This study provides a detailed ecological assessment of the Mula-Mutha River, Pune, integrating physicochemical water quality parameters with avian diversity as bioindicators across three hydrological seasons—pre-monsoon, monsoon, and post-monsoon. Water samples collected from upstream to downstream sites were analyzed for pH, dissolved oxygen (DO), biochemical oxygen demand (BOD), chemical oxygen demand (COD), turbidity, nitrate, and phosphate concentrations. Simultaneous avian surveys using point count and direct observation methods were assessed through Shannon-Wiener and Simpson’s diversity indices. Seasonal variations were significant: pre-monsoon exhibited low DO (5.1 mg/L) and high BOD (8.9 mg/L), indicating organic enrichment, while post-monsoon showed improved water quality (DO 7.5 mg/L; BOD 5.2 mg/L) due to hydrological recovery. Avian richness peaked in postmonsoon (55 species; H′ = 3.35) and was lowest during pre-monsoon (38 species; H′ = 2.71), strongly correlating positively with DO and negatively with BOD and phosphate levels. Dry-season proliferation of invasive macrophytes (Eichhornia crassipes, Pistia stratiotes) exacerbated hypoxia, reducing piscivorous bird activity. These findings confirm avian diversity as a robust bioindicator of river health and highlight the urgent need for pollution control and habitat restoration measures within the Mula-Mutha river at Pune urban area.