Wetland ecosystems are essential for maintaining biological diversity and are significant elements of the global landscape. However, the biodiversity of wetlands has been significantly reduced by more than 50% worldwide due to the rapid expansion of urban areas and other human activities. The aforementioned factors have resulted in drastic antagonistic effects on species composition, particularly aquatic avifauna. The decline in wetland avifauna, which can be attributed to changes in water quality that impact aquatic habitats, is a major concern. In this study, we evaluated the impact of physicochemical parameters on aquatic avifauna in India’s first Conservation Reserve, a Ramsar site and an Important Bird Area. Water samples were collected on a monthly basis across nine different sites and various parameters, such as temperature, electrical conductivity, pH, biological oxygen demand, dissolved oxygen, total dissolved solids and salinity, were analyzed for pre-monsoon and post-monsoon seasons, while point count surveys were conducted to assess species richness and the density of waterbirds. Our findings show a positive correlation of species density with water temperature (r = 0.57), total dissolved solids (r = 0.56) and dissolved oxygen (r = 0.6) for pre-monsoon season and a negative correlation for dissolved oxygen (r = −0.62) and biological oxygen demand (r = −0.69) for post-monsoon season. We suggest that a synergistic effect of pH, salinity, biological oxygen demand and total dissolved solids may affect aquatic bird populations in Asan Conservation Reserve. Poor water quality was observed in a few sampling sites, which may negatively affect the number and density of waterbirds present. The findings of this study emphasize the importance of water quality in wetland conservation, particularly for aquatic avifauna.