Anaerobic microbial communities in the anoxic zones degrade organic matter in estuarine sediments. Thermodynamic energy yield for the oxidation reactions with various electron acceptors decreases in the order of O2> NO3- > Mn4+> Fe3+> SO42- > CO2. The predominant terminal electron accepting (TEA) process has an influence on the biogeochemical cycles of nutrients as well as the production of important greenhouse gases such as nitrous oxide and methane from estuarine sediments. The research questions of this study were (1) what are the environmental factors (pH, salinity, organic carbon, sulphate, redox potential) explaining variability in TEA activities such as nitrate reduction rate (NRR), iron reduction rate (IRR), sulphate reduction rate (SRR) and methane production rate (MPR) and (2) which is the predominant TEA process during degradation of organic matter. To determine the TEA activities, sediment samples collected from 13 sampling stations of Ashtamudi estuary during monsoon 2014 and summer 2015 were incubated with sulphate depleted artificial seawater, under anaerobic conditions for 72 h, in microcosms. Spatial variations dominated temporal variations for environmental variables. Nevertheless, biogeochemical processes showed a distinct seasonal variation. Total TEA activity was higher during summer than monsoon, indicating the higher heterotrophic microbial activity favored by high temperature. Individually, SRR was the maximum during summer, while NRR, IRR and MPR were the maximum during monsoon. Sulphate reduction was observed to be the predominant electron accepting process in all sampling stations with cumulative values of 3125.79 and 4046.07 nmol cm-3 day-1 during monsoon and summer respectively. This was followed by NRR, IRR and MPR. Although thermodynamically more favorable, NRR could not predominate due to scarcity of nitrate in sediments. Nevertheless, two-fold and five-fold increase in methanogenesis and denitrification were observed respectively during monsoon in sampling stations, which cannot be ignored, owing to the importance of methane and nitrous oxide as a potent greenhouse gas.