Variation of polysaccharide concentration in irrigation-channel sediment was determined concurrently with biological, chemical and physical factors influencing the benthic algal community. Phenol-sulphuric acid method was used to measure polysaccharide concentration. Polysaccharide concentration, biomass of benthic algae, and species composition changed spatially and temporally. Fluctuations of total suspended solid (TSS) concentration and exposure of channel bed to direct sunlight had major effects on algal growth and polysaccharide production. Polysaccharide concentration was correlated to chlorophyll a concentration (r = 0.73, P<0.001) and algal biomass (r= 0.57, P<0.001). Fragilaria construens and Aulacoseira (Melosira) italica were the most common diatoms in the benthic flora. Chlorophyll a concentration in the sediment showed a strong negative correlation (r= -0.99, P<0.001) with the seasonal variation of TSS concentration in channel water.The polysaccharides produced by benthic microorganisms play a major role in clogging channel bed and thereby reducing seepage from earthen irrigation channels. Correlations between polysaccharide concentration and chlorophyll a (and algal biomass) further indicate the importance of benthic algae for polysaccharide production. Since availability of light to the algal flora is critical for the production of polysaccharides, the effect of clogging can be maximized by exposing the channel bed to direct sunlight during non-irrigation period (winter).