The ecological water quality in rivers and streams is influenced both by the morphological factors (within the watercourse channel and by the dynamic factors associated with flow), as well as biological factors (connected with the flora and fauna characteristic of its specific area). This paper presents an analysis of the effect of river channel shading by trees and shrubs on hydromorphological changes in a selected reach of the Wełna River, Poland. The analysis was conducted on two adjacent cross-sections (one in a reach lined with trees, the other in an open area with no tree or shrub vegetation). Data were collected during field surveys in the years 2014 and 2019. According to the Water Framework Directive, the Wełna River represents a watercourse with small and average-sized watershed areas, with sand being the dominant substrate of the river bottom. Flow volume, distributions of velocity in the sections, as well as substrate grain-size characteristics and river bottom morphology, were determined based on field measurements. In the study, the leaf area index (LAI) of vegetation was measured in the reach lined with trees, while the number and species composition of macrophytes were determined in the investigated river reaches. Moreover, a digital surface model (DSM) and Geoinformation Information System GIS tools were used to illustrate variability in shading within the tree-lined reach. The DSM model was based on Light Detection and Ranging (LIDAR) data. The results of this study enable us to establish the relationship between river shading by vegetation covering the bank zone, and changes in hydromorphological parameters of the river channel.