The impact of the nutrient level on the water quality in the Hooghly and Matla estuarine complex in Indian Sundarbans was assessed for three decades (1984-2014). Nitrate, phosphate and silicate were used as indicators of nutrient related water quality in the estuarine water. Our first order analysis reflects significant spatio-temporal variations of selected nutrients with relatively higher values in the Hooghly estuary (in the western Indian Sundarbans) compared to the Matla estuary (in the central Indian Sundarbans). Significant variations were observed in dissolved nitrate, phosphate and silicate concentrations between stations and years (p < 0.01). Such pronounced variations may be attributed to the location of highly industrialized and urbanized city of Kolkata, Howrah and Haldia port-cum-industrial complex adjacent to the Hooghly estuary. The sudden rise of selected nutrients during premonsoon, 2009 (irrespective of sampling stations) is directly related to AILA, a super-cyclone that occurred in the lower Gangetic delta during 22nd-25th May, 2009. © 2015 Jordan Journal of Biological Sciences.