Ashtamudi is the second largest estuary in Kerala covering an area of 32 Sq. km. Surface and bottom water characteristics from 4 stations have been analysed in the context of pollution from a paper mill effluents. The primary productivity, distribution and abundance of zooplankton and benthos have been studied in detail. The average annual gross and net productivities in the surface water was maximum at Neendakara (St. 1) and minimum at Kadapuzha (St. 4). The zooplankton community consisted of 21 taxa, among them copepods constituted the most abundant group. Benthic fauna (56.95%) for the whole year was observed at Station 1 and lowest at St. 4 (0.87 %). The study has brought to light the nature of impact oi' pollution in one of the productive estuaries in Kerala.