Macrophytes are one of the biological elements for assessing the ecological status. Macrophyte communities were studied in six artificial (drainage canal and ditches) or modified watercourses (regulated rivers). In order to assess the ecological status of the watercourses, studies were carried out with the use of the Macrophyte Index for Rivers (MIR) proposed in the Water Framework Directive. Macrophyte communities were mainly represented by helophytes (12 species in total), and the highest percentage area cover (50–75% of the site) was observed for pleustophytes (Lemna spp.). Macrophytes communities were affected by the gradients of hydromorphological (canal modification, flow type, and shading) and parameters water quality (nutrients and water transparency). The relationships were highly species-specific. In accordance with the MIR values, the ecosystems were classified as having poor (drainage canal), moderate (regulated rivers), or good (drainage ditches) ecological status.