The aim of the study was to develop a technique for evaluation of transboundary water pollution. A method for evaluation of transboundary water quality was worked out. The method is based on calculation of the chemical index and classification of the water quality. It includes the measurement of several chemical parameters in water samples. The combination of the results is then represented as the chemical index CJ, which stands for the generalized water quality. A relative weight W is determined for each parameter. This weight can be considered as the priority level of each parameter. Then the value of the sub-index q is determined for each parameter with the help of digitized calibration graphs. The chemical index of water pollution CJ is the multiplicative function of sub-indexes q in the degree equal to the relative weight of each parameter. Also, a classification system was produced for the pollution assessment of transboundary water bodies based on the ‘broken stick’ model. Water quantity was grouped into five classes. The suggested technique was applied to reveal changes in the water quality of the transboundary Lake Peipus from 2000 to 2015 year. The water in this period is generally classified as “low polluted” (quality class 2). The chemical index CJ varied from the minimal 89.9 in 2003 to the maximal 96.8 in 2013