This paper shows the results of a study on the morphometric, hydrophysical, and hydrochemical indicators of Lake Burabay, North Kazakhstan. The Burabay Protected Area, also known as Burabay National Park or Kokshetau National Park, is a protected natural area located in the north of Kazakhstan. It encompasses a diverse landscape characterized by lakes, forests, and unique rock formations. This analysis includes an eco-toxicological assessment of the hydrochemical composition of waters and benthal deposits by studying the content of metals. The degree of mineralization, ionic composition of water, hydrogen index, pollution index, and water quality class were also determined. Reductions in the area and depth of the lake were identified. The pollution index is 1.5–1.7, which belongs to class 3—moderately polluted. Relatively high concentrations of cadmium, nickel, copper, and arsenic were found in the lake sediments. Therefore, Lake Burabay and its surrounding ecosystem face certain environmental risks and potential water pollution. Although the increase in the number of tourists did not have a significant impact on the water pollution index in Lake Burabay, some of the common threats that impact the area are induced by touristic development, agricultural practices and industrial pollution. Significant efforts should be made to reduce these risks using the environmental indicators as a reference for control environmental quality.