UE regulations focus on methods of water quality monitoring and their use in rational management practices. This study investigated horizontal and vertical variations of electrical conductivity (EC), pH, dissolved oxygen (DO), and chlorophyll a (Chl-a) in a shallow polymictic lake. Monitoring of short-term variability of physical and chemical lake water parameters is a critical component in lake management, as it influences aquatic life. Based on the field research, maps of spatial distribution of the parameters were drawn. Using two methods: (1) a classical approach to water column measurements, from the top to the bottom (TB), in which the reference point is always a surface layer (SL), and (2) a newly introduced method of lake water quality monitoring based on a nearest neighbor (NN) approach; a comparison of higher and lower layers of the water column. By subtracting partial maps of spatial variability for different depths, final raster images were obtained. The NN method is rather absent in the limnology literature worldwide. Vertical and horizontal variability of the tested parameters in the polymictic, shallow Lake Bikcze (Poland) was presented in the results. In the presented paper, the commonly used TB method emphasized the role of the surface layer in shaping the variability of physicochemical parameters of lake waters. It shows a general trend of parameters’ changes from the top, to the bottom. The newly presented NN method, which has a major advantage in its simplicity and objectivity, emphasized structural differentiation within the range of variability. The nearest neighbor method was more accurate in showing the actual structure of fluctuation of parameters with higher fluctuation in the water column. Its advantage is a detailed recognition of the vertical variability of selected parameters in the water column. The method may be used regardless of the lake depth, its location in climatic zone, and/or region