The subject of this thesis is a description of various types of mathematical models aimed at the spread of pollution in the river downstream and selection of the most suitable type of model and design the new one with using MATLAB. The application of the model is performed on Karlický creek, where it will be put into operation a new wastewater treatment plant Vysoký Újezd. Using the assembled model there are presented three simulation studies showing the dependence of time on the concentration of nitrate. These are:  Simulation of accident of the wastewater treatment plant Vysoký Újezd  Excessive intake of nitrate caused sheet erosion from adjacent agricultural land  Combination of both simulations Individual studies present the effect of nitrate on the water quality in Karlický creek, which falls into two categories of protection, Český kras area and Nature Reserve Karlické údolí. The aim of the above simulation studies is to demonstrate the spread of the nitrate into the various compartments along the entire length of the watercourse, and to show the loss of the nitrate over time and to compare the effects of point and diffuse sources of pollution. The model is calibrated according to the samples taken in Karlík creek during the period from 30 June 2008 to 31.12. 2009th . The results of...