Primary productivity at four representative stations in the Ashtamudi estuary has been presented. The average gross and net productivities in the surface water was maximum at Neendakara, the bar mouth zone and minimum at Kadapuzha, the riverine zone consistently exposed to pollution from paper mill effluents. Ashtamudi, the station directly on the gradient line and Kanjirakode, the station equidistant from Kadapuzha and Ashtamudi presented a transition phase with regard to the primary productivity. In the bottom water also productivity was minimum at the polluted zone. Generally productivity at sub-surface levels was higher than that at the surface. A seasonal pattern, independent of various environmental parameters, was discernible both in the gross and net productivity changes at surface and sub-surface levels. High concentrations of dissolved oxygen, silicate and nitrite helped to maintain higher productivities at Neendakara, Ashtamudi and Kanjirakode on several occasions during the year. The fact that productivity at the polluted Kadapuzha station was the lowest, indicates that the paper mill effluent has considerably disturbed the productivity mechanism of this otherwise healthy ecosystem.