The present study demonstrates the recovery of phytoplankton assemblage from metal stress. Phytoplankton assemblage consisting of different freshwater algal species isolated from a tropical pond was exposed to sublethal concentrations of Cu and Zn for 25 days in semi-continuous culture (Toxicity phase). Subsequently, algal assemblage grown in the toxicity phase were transferred to the fresh culture medium without elevated levels of the test metals for 25 days in semi-continuous culture (Recovery phase). We monitored the total biovolume of each algal species during the toxicity and recovery phases. The members of Cyanophyta were most sensitive against metal toxicity, followed by the members of Bascillariophyta. However, the members of Chlorophyta showed relatively lesser sensitivity against test metals. Among chlorophytes, Scendesmus opolinensis and Cosmarium bioculatum were tolerant to both the test metals. Metal-stressed algal species showed recovery after transferring to the basal medium depending on the concentration of metals during the toxicity phase. The members of Cyanophyta were unable to recover from metal stress. However, members of Chlorophyta showed faster recovery than others from Zn stress, and the members of Bascillariophyta showed quicker recovery from Cu stress. The differential abilities of various algal species to recover from metal stress perhaps depend on their ability to counterbalance metal toxicity. Further, research is warranted to characterize the differential ability of various algal groups to recover from metal stress. The present findings would help understand the efficiency of different algal groups to restore their position within the freshwater algal community after the disappearance for metal stress.