As a renewable energy source, microalgae have wide interest as a potential tool to produce biofuel and bioproducts. Prevailing in the local habitat, indigenous microalgae are more successful for wastewater treatment processes. Integrated microalgae-based biofuel and bioproduct production with wastewater treatment is a successful practice of modern research. This report describes the isolation and identification of 61 microalgal strains from lakes, springs, ponds, creeks, and rivers of the gigantic area of Malakand, Pakistan. Our study involves the seasonal existence of Chlorophyta in the area, with most dominant flora identified in the summer season followed by spring, autumn, and winter seasons, respectively. The highest ratio of microalgae was found in stagnant waters followed by slow-running water and running water, respectively. However, algal species were reported from all water bodies throughout the year. Commercially important genera like Chlorella, Scenedesmus, and Chlamydomonas were also reported, attracting the research area for further analysis regarding biofuel, bioproduct production, and simultaneous wastewater treatment.