This paper presents changes in the flow of 14 rivers located in the Warta River basin, recorded from 1951 to 2020. The Warta is the third-longest river in Poland. Unfortunately, the Warta River catchment area is one of the most water-scarce regions. It hosts about 150 hydropower plants with a capacity of up to 5 kW. The catchment areas of the 14 smaller rivers selected for the study differ in location, size, land cover structure and geological structure. The paper is the first study of this type with respect to both the number of analyzed catchments, the length of the sampling series and the number of analyzed flow characteristics in this part of Europe. The analysis of changes in the river flows was performed with reference to low minimum, mean and maximum monthly, seasonal and annual flows. Particular attention was paid to 1, 3, 7, 30 and 90-day low flows and durations of the flows between Q50 and Q90%. In addition, the duration of flows between Q50 and Q90% were analysed. Analysis of the direction and extent of particular flow types was performed by multitemporal analysis using the Mann–Kendall (MK) and Sen (S) tests. The analysis of multiannual flow sequences from the years 1951–2020 showed that the changes varied over the time periods and catchments. The most significant changes occurred in the low flows, while the least significant changes occurred in the high flows. From the point of view of the operation of the hydropower sector, these changes may be unfavourable and result in a reduction in the efficiency of run-of-river hydropower plants. It was established that local factors play a dominant role in the shaping of river flows in both positive and negative terms, for the efficiency of the hydropower plants.