Pallathuruthy is a meeting point between Pamba River and Vembanad Lake of Kerala, South India. So it is an estuarine habitat. The present study analyses the seasonal variation in fish faunal diversity and its relation with existing water quality parameters through cluster analysis. The study showed that there was significant variation in diversity and fish catch strength between three seasons like pre monsoon, monsoon and post monsoon. High species diversity was observed during monsoon season, while good catch strength was obtained during post monsoon. Results of water quality analysis have showed that TDS, Copper, chromium, cadmium and lead content in water were beyond the limit set by IS (2012). Also regarding the sediment quality the cadmium content was above the threshold effect level prescribed by Canadian Sediment Quality Guidelines for the Protection of Aquatic Life (2001). So, urgent measures were inevitable to sustain the existing fish wealth of this estuarine area.