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Spatio-temporal and seasonal variation of the water quality characteristics of the Hooghly River Estuary, India were studied considering eight stations of diverse eco-hydrological characteristics. Wide variations in turbidity, total dissolved solids and fecal coliform exceeded the permissible BIS drinking water level limit. The estuary is observed to be relatively low-oxygenated, mesotropic and phosphate limiting. Spatial heterogeneity and impact of the southwest monsoon were remarkably pronounced in the distribution of the inorganic nutrients revealing the following values (expressed in μg atm l − 1 ): nitrate + nitrite (2.42–37.19), phosphate (0.41–1.52) and silicate (38.5–187.75). Water Quality Index (WQI) values confirmed the prevailing ‘bad’ condition, detrimental for sustenance of aquatic biota. Results of Principal Component Analysis identified the major factors liable for water quality deterioration while cluster analysis categorized the stations on the basis of similar water quality status. The authors recommend adopting preventive measures for water quality improvement linked to biodiversity conservation. [ABSTRACT FROM AUTHOR]