Monthly variation of plant pigments such as chlorophyll - a and phaeopigments were studied for one year from Feb. 1998 to Jan. 1999 in the brackishwater impoundment of Nethravathi estuary, Mangalore. Chlorophyll - a values fluctuated from 0.037 mg/g sediment (Nov) to 2.10 mg/g sediment (Feb). It exhibited trimodal pattern of distribution with primary peak during February followed by December and July. Phaeopigment concentration ranged from 0.064 mg/g sediment (Nov) to 13.71 mg/g sediment (Aug). Chlorophyll - a values showed significant correlation with benthic phytoplankton whereas it is inversely related with sediment nitrogen and phosphorus.