An assessment of plankton distribution and physical and chemical parameters was undertaken in different altitudinal lakes of Arunachal Pradesh. The sampling and data analysis was performed following standard methods. Out of the total 66 species recorded, 15 species commonly occurred. Amphora sp., Bulbochaete sp., Closterium sp., Cymbella sp., Lyngbya sp., Mougeotia scalaris , Navicula sp., Nitzschia sp., Oedogonium sp., Pinnularia sp . , Spirogyra sp., Stauroneis sp., Surirella sp., Synedra sp. and Zygnema sp. commonly occurred. Ganga Lake recorded the highest 33 species while Bone recorded the lowest 7 species. Bacillariophyceae was dominant representing 22 species while Chrysophyceae, Dinophyceae, Euglenophyceae, and Klebsormidiophyceae recorded only 1 species each. We found slight variations in physical and chemical properties due to altitude. The conductivity ranged between 4μS/cm (Kyalem) to 60μS/cm (Bone); total dissolved solid between 5mg/l (Sela) to 22mg/l (Mehao); pH between 6.8 (Mehao) to 9.3 (Hireng); highest dissolved oxygen between 4.77 mg/L (Kyalem) to 15.4 mg/L (Hireng); free carbon dioxide between 0.23 mg/L (Ganga) to 1.2 mg/L (Nagula); alkalinity between 3.4 mg/L (Mehao) to 8.2 mg/L (Hireng) and hardness between 3.7 mg/L (Mehao) to 17 mg/L (Pegu). The findings provide baseline data on phytoplankton distribution and water quality of different altitudinal lakes in the Arunachal Himalayan Region.