The seasonal investigation about the water quality from Damanganga river estuary on two habitats downstream and upstream was carried out from January to December 2019 containing three major seasons: winter, summer and monsoon. For this monitoring activity total 29 parameters (24 physico-chemical parameters and 5 heavy metals) were analyzed. Multivariate analyses suggested inter dependency among these studied parameters. Water Quality Index is computed based on the major fluctuated and affected parameters. The calculated values of WQI for all three seasons ranged from 122.84 to 173.82 which suggested poor water quality of the water body. WQI values of the investigation area proposed that the estuarine water quality is deteriorated due to high value of presented heavy metals (Aluminum, Iron, Manganese, Boron and Zinc), Chloride, Ammonium and Sulfate in water sample. In this case, the downstream station is having accessional pollutant contaminations while the upstream station is having diminutive pollutant contaminants. Temporally, the dominant frailty found during the winter followed by summer and monsoon. This study field exhibited poor quality of water; the reason behind this might be the impressive surrounding industrial zone as well as other anthropogenic activities. There is quite normal probability distribution expressed by the represented water quality data at the both habitats. The Bray-Curtis cluster analysis shows different percentage similarity level between the water quality parameters.