Agricultural practices have a significant impact on stream water quality in rural landscapes; however, there is still little empirical evidence of how different types of cultivation alter the hydrochemistry of running water. Thus, the current study explored the spatial dynamics of selected ion concentrations and their land cover dependence in lowland agricultural catchments. From November 2021 to October 2022, water samples were collected from 30 sites located across small tributaries of the rivers Bzura, Pilica, and Radomka for chemical analysis of their NO3, NO2, NH4, Ca, Mg, K, Na, As, Ba, Sr, and V concentrations. The results indicated a clear spatial heterogeneity of water quality, related to lithology and dominant land cover evaluated with the CORINE Land Cover 2018 dataset. Overall, sites representing agricultural land promoted increased concentrations of major and trace elements, while those with pepper cultivation were additionally contaminated with NO3 and NO2. The correlation performance for nitrogen compounds was the highest for narrower buffer zones, which was not documented for major and trace elements, which were linked more strongly with land cover at larger scales. Such new insights into the water quality dynamics of lowland agricultural catchments, being a simultaneous reflection of lithology, agricultural practices, and several municipal impacts, have significant implications for appropriate water management in rural landscapes.