Paddling benefits people's health and wellbeing but can impose pressure on aquatic ecosystems. Negative effects intensify if many recreationists simultaneously use the same waterbody, sites, or sections and at high intensity. Therefore, especially waterbodies attracting high numbers of people are threatened to become ecologically degraded. We examined effects of paddling on aquatic macrophytes in waterways of the Spreewald biosphere reserve, one of the most popular destinations for water tourism in Germany. Nine waterway sections were investigated with varying boating intensity gradients from low to highly frequented with medians of 1 to 239 boats per day, respectively. Mechanical damage to emergent vegetation increased with boating intensity depending on waterway width: Observed overall and group-specific damage decreased at widths > 15 m despite high paddling intensity. Diversity (species richness and Shannon-index) decreased with increasing boating intensity; however, in at least one waterway less shade has masked boating effects resulting in high plant diversity despite high paddling intensity. Overall, plant damage and diversity effects were more pronounced between closed reference waterways and open paddling waterways than between the intensity gradients studied, suggesting that critical impacts were already reached at moderate paddling frequency. Furthermore, paddling significantly shaped species composition between sites, and had stronger negative effects on submerged than on emergent macrophytes, and on rigid than on flexible growth forms. In waterways open for boating, where potential contact with paddle strokes or canoe hulls is high, the growth of rigid, less flexible plant species was impaired. In contrast, submerged species with flexible stems and branches, soft leaves, and reproducing from fragments were found independent from boating intensity. Further, waterways closed for boating provided refugia and regeneration niches indicated by rare or endangered species more frequently found therein.