Heavy metals and other organic pollutants are the hazardous materials causing soil and water pollution, hence, bioremediation of these components is a matter of concern for environmental biotechnologists. Twenty one microalgal and cyanobacterial strains were evaluated for removal of copper from aqueous solutions and soil containing 10 ppm copper. 5 out of 21 strains have shown comparatively higher tolerance to copper stress. The biosorption capabilities of all the five strains were assessed using techniques like ultraviolet (UV) spectrophotometers, scanning electron microscope (SEM), inductively coupled plasma mass spectrometry (ICP-MS), and confocal Microscopy. It was found that the five selected strains could grow normally upon incubating with 20 ppm of Cu. Copper removal efficiencies of these microalgae (S. obliquus, A. braunii, C. fusca, L. JSC-1 and C. saccharophila in water were 99.9, 99.3, 97, 96.7, and 96%, while for soil was 73, 75, 71, 70, 68%, respectively. A minor leakage of nucleic acid and protein were detected with time. Furthermore, no any visible morphological changes were observed after six days of treatment, while minor changes were noticed after 12 days in water, and severe morphological deformations occurred after 24 days of bioremediation in soil. Our findings reveal that the selected microalgal strains have high potential for Cu bioremediation at certain concentration for 12 days exposure from water and 24 from soil.