We investigated changes in the spatial distribution of phosphorus (P) and nitrogen (N) in the deep, mesotrophic Lake Hańcza. The raw data collection, supported by global navigation satellite system (GNSS) positioning, was conducted on 79 sampling points. A geostatistical method (kriging) was applied in spatial interpolation. Despite the relatively small area of the lake (3.04 km2), compact shape (shore development index of 2.04) and low horizontal exchange of water (retention time 11.4 years), chemical gradients in the surface waters were found. The largest variation concerns the main biogenic element – phosphorus. The average value was 0.032 at the extreme values of 0.019 to 0.265 mg L−1 (coefficient of variation 87%). Smaller differences are related to nitrogen compounds (0.452–1.424 mg L−1 with an average value of 0.583 mg L−1, the coefficient of variation 20%). The parts of the lake which are fed with tributaries are the richest in phosphorus. The water quality of the oligo-mesotrophic Lake Hańcza has been deteriorating in recent years. Our results indicate that inferences about trends in the evolution of examined lake trophic status should be based on an analysis of the data, taking into account the local variation in water chemistry.