Lakes are vast bodies of water that are encircled by land and home to a variety of aquatic life forms. They are impacted by both natural and man-made environmental processes. The present research aimed to determine the physicochemical properties and phytoplankton community in Karna Lake (Haryana) and Khajjiar Lake (Himachal Pradesh). Phytoplankton plays a vital role in the aquatic food chain, particularly for zooplankton. Water samples were collected from both lakes, i.e., from October 2023 to September 2024. Temperature, pH, conductivity, free carbon dioxide, chlorides, total hardness, biochemical oxygen demand, dissolved oxygen, alkalinity, sodium, potassium, phosphate, acidity, nitrate, were analyzed for both lakes. The physicochemical analysis indicated significant geographical and seasonal variations between the sampling sites. The water temperature fluctuated from 12.14 ± 4.21 °C to 20.05 ± 7.53 °C, and the pH remained slightly alkaline (7.23 ± 1.02 to 8.08 ± 0.03). Conductivity readings ranged from 266.17 ± 35.27 μS/cm to 413.50 ± 54.18 μS/cm, with greater values seen in Karna Lake. Dissolved oxygen concentrations ranged from 6.01 ± 2.32 mg/L to 9.26 ± 2.16 mg/L, while biological oxygen demand was 1.32 ± 1.66 mg/L to 3.59 ± 1.74 mg/L. Karna Lake had greater levels of nitrate (1.8 ± 0.389 mg/L) and phosphate (0.61 ± 0.41 mg/L), indicating nutrient enrichment. Statistical investigations revealed that conductivity, nitrate, phosphate, temperature, and biological oxygen demand were the most important environmental variables impacting phytoplankton dispersal. During the study period, 24 phytoplankton species were recorded by family, including Bacillariophyceae (10 species), Desmidiaceae (2 species), Cyanophyceae (6 species), Chlorophyceae (4 species), and Euglenaceae (2 species). The work emphasizes the ecological significance of phytoplankton as bioindicators of freshwater ecosystem variability and provides baseline limnological data for future monitoring and protection of lake ecosystems.