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A study was conducted to understand the intra- and inter-seasonal variability of dissolved oxygen and nutrients in a tropical monsoon estuary (Zuari in Goa, India). We adopted a dual sampling approach with (a) daily or alternate day sampling at a fixed location in the mid-estuarine zone and (b) longitudinal transect sampling from freshwater end to mouth during spring and neap tides of each month for about a year. Multivariate statistical analyses of oxygen and nutrients were carried out to evaluate the hypotheses: (i) biogeochemical processes chiefly regulate their variability and (ii) anthropogenic inputs lead to material accumulation in the estuary. Multivariate statistical analyses helped identify the controlling factors of the oxygen and nutrient variability. Our results significantly revealed (i) physical forcings (freshwater discharge and tidal circulation, these also facilitate sedimentary releases) are more important than biogeochemical processes in determining oxygen and nutrient variability in the water column and (ii) the monsoon driven regular annual flushing makes the system resilient to human interference as the Zuari estuary returns to normalcy by postmonsoon every year. Our study identified the significance of subsurface discharges in transporting mining effluents from the river basin. Results also suggest that extrapolation of controlling factors of biogeochemical variables at a fixed location to the entire estuary is untenable since the relative dominance of forcings vary in time and space in the estuary.