Lake Uluabat is dependent on the RAMSAR Convention (the Convention on Wetlands of International Importance, especially as waterfowl habitat) which was accepted in Iran in 1971 as a member of Living Lakes network carried out by the Global Nature Fund. The lake is very important in terms of biodiversity. Relationships of physicochemical parameters of lakewater and sediment with chemical fractions of heavy metals (chrome and nickel) in lake sediments were investigated in Lake Uluabat in Bursa, Turkey. The concentrations of Cr and Ni forms (dissolved, particulate, total sediment, sediment fractions) and other water and sediment quality parameters were assessed monthly at 10 sampling points between August 2013 and July 2014. The results demonstrate that the concentrations of water and sediment quality parameters undergo monthly changes. The geoaccumulation (Igeo) index has been widely applied to the assessment of sediment contamination. According to this index, Lake Uluabat has moderately polluted sediment. Cr and Ni concentrations in sediment have been determined to be higher than the upper effect threshold according to international standards. Variations of the fractions of Cr and Ni bound to organic matter (F4), residual, and bound to Fe-oxide fractions (F5) were found to be the most dominant forms. Mostly, all forms of Cr and Ni were significantly and positively correlated with pH, electrical conductivity, and suspended solids. The results revealed the importance and the need for strict control of point and non-point pollution loads for the preservation of Lake Uluabat’s water and sediment quality.