The detection of non-point pollution in large rivers requires high-frequency sampling over a longer period of time, which, however presumably provides data with large spatial and temporal variance. Variability may mean that data sets recorded upstream and downstream from a densely populated area overlap, suggesting at first glance that the urban area did not affect water quality. This study presents a simple way to explore trend-like effects of non-point pollution in the Danube based on data that varied strongly in space and time. For one year, biweekly sampling was carried out upstream and downstream from a large city with negligible emission of untreated wastewater and the surrounding settlements, industrial and agricultural areas.Although most of the values of the 34 examined physicochemical characteristics fell within the range of data previously published for the Danube, and the mean values of all parameters indicated unpolluted surface water, different water quality was revealed upstream and downstream from the metropolitan area at each sampling time. Since the physicochemical characteristics causing the separation also differed from time to time, univariate tests and consensus ordination were used to determine which variables changed similarly during most of the examined period. With this evaluation method, several diffuse pollutants of anthropogenic origin contaminating the Danube in the long term were identified, such as nitrogen, phosphorus, sulphate, chloride, potassium and vanadium. The results demonstrated that trend-like effects of non-point pollution can be detected even in a large river, where physicochemical measurements can vary strongly in space and time.