Abstract The combined effects of seasonality and in situ heavy metal (Cu, Zn, Pb) enrichment on periphyton in a large river was experimentally studied using metal-diffusing substrates Highest release rate and intracellular accumulation of metal ions (Cu, Zn and Pb) was examined in rainy and summer seasons, respectively. Release rate and intracellular accumulation showed the following order: Zn > Cu > Pb in the three seasons. Periphytic algae growing on these substrates showed intracellular accumulation of test metals (Cu, Zn and Pb) which inhibited growth in a concentration dependent manner, as evidenced by reduced cell number, species richness and Shannon index of the community. Concentration dependent decrease in Chlorophyll a and rise in Caro./Chl a ratio was found under Cu and Zn stress. Periphytic community in summer and winter was found similar than rainy season and was found be dominated by diatoms followed by green and cyanobacteria. In comparison to green algae and cyanobacteria, diatom species, showed relatively higher % relative abundance under heavy metal stress than their respective control. Increased lipid body production and cell wall deformities in diatoms were found under Cu and Zn stress but not under Pb stress, possibly because Pb diffusion from the substrates was low. After 28 days of diffusion, metal release rates were near the control levels and periphyton parameters had recovered, demonstrating rapid response to changing conditions by the periphyton. The rapid recovery of the periphyton (within 14 days) indicates that periphyton biomonitoring may be useful for not only monitoring of stable conditions but also for changing conditions, such as monitoring recovery. The present study shows the utility of metal diffusing substrate and periphytic diatom community as an effective tool for biomonitoring (including recovery) of heavy metal pollution in the fluvial ecosystem.