Two years (2003-05) study was undertaken to examine the periodic changes in heavy metal loads in waters and sediments of seven natural lakes viz., Bhimtal, Naukuchiatal, Punatal, Sitatal, Ramtal, Hanumantal and Nainital, Uttaranchal, India. Water samples were collected during summer, autumn, winter and spring seasons while sediment samples were collected during summers of both years. The relationships between the concentrations of heavy metals in waters and physico-chemical properties of water and also with different chemical fractions of metals in sediments were evaluated. The pH, electrical conductivity, dissolved oxygen, biological oxygen demand and bicarbonate alkalinity in waters were in the range of 7.69-8.63, 0.07-0.63 dS. m-1, 3.12-9.66 mg. L-1, 0.43-2.96 mg. L-1, 65.1-373.1 mg. L-1 and 53.1-296.4 mg. L-1, respectively. The sediment samples have pH, electrical conductivity, readily oxidizable C, total C and CaCO3 equivalent in the range of 7.81-8.99, 0.093-0.232 dS. m-1, 0.18-1.06 %, 0.55-2.38% and 2.64-37.74 %, respectively. The concentrations of Cr, Mn, Fe, Ni, Cu, Zn, Cd and Pb in waters of different lakes varied in the range of 0.29-2.39, 10.3-38.3, 431-1407, 1.0-6.6, 5.3-12.1, 12.6-166.3, 0.7-2.7 and 3.9-27.1 µg. L-1 and in sediments 14.3-21.5, 90.1-197.5, 5265-6428, 17.7-45.9, 13.4-32.0, 40.0-149.2, 11.1-14.6 and 88.9-167.4 µg. g-1, respectively. Except for Fe, the concentrations of all metals in waters were found to be well below the toxic limit prescribed by different agencies. As regards seasonal variations, the concentrations of the most heavy metals were found to be the highest during summers of both years. The concentrations of Cr, Mn, Ni, Cu, Zn, Cd and Pb were significantly and positively correlated with pH, Electrical Conductivity (EC), Biological Oxygen Demand (BOD), Chemical Oxygen Demand (COD) and alkalinity of waters but negatively correlated with Dissolved Oxygen (DO). The concentrations of Cr, Ni, Zn, Cd and Pb in waters were significantly and positively related with water-soluble + exchangeable fraction of these metals in lake sediments. The concentrations of Zn, Cd and Pb in waters were significantly and positively correlated with carbonate bound fraction of these metals in lake sediments. The concentrations of Cr, Mn, Fe, Cu, and Pb in waters were significantly and positively correlated with organically bound fraction of these metals in lake sediments. The concentrations of Cr, Mn, Ni, Cu and Zn in waters were significantly and positively correlated with reducible fraction of these metals in lake sediments. All heavy metals except Cd in waters had a significant direct correlation with residual fraction and total content of these metals in lake sediments.