Due to their small size and high anthropogenic pressure, small watercourses are particularly prone to severe siltation and are densely overgrown with macrophytes. Many of these watercourses are subject to regular maintenance works (RMW), consisting of seasonal desilting and vegetation clearance, in order to ensure unobstructed water flow. The aim of the study was to assess the impact of three types of maintenance works: dredging and mud removal (DMR), river channel vegetation removal (RCVR) and river bank vegetation removal (RBVR) on taxa species richness, macroinvertebrate density and the Shannon-Wiener diversity index, as well as their changes and long-term benthic recolonization one and two years after completion of the works. The study was carried out in 21 habitats on eight rivers in the European Central Plains Ecoregion. A total of 107 zoobenthic taxa were found at all sites, and their species composition was characteristic of highly hydrophytic waters with low hydrological and hydrochemical quality parameters. A significant decrease in macroinvertebrate taxa richness was observed one year after the works, as the average number of taxa had dropped from thirteen to eight, with a further fall to seven taxa two years after the RMW. The same was true for density, which had decreased from an average of 2496 to 786 individuals per square meter one year after the RMW, while, a gradual recolonization was recorded two years after the RMW, with an average density of 1295 individuals per square meter. The Shannon-Wiener index, which had averaged 2.528 before the RMW, also decreased, falling to 1.982 and 1.832 one and two years after. BACI statistical analyses showed that of the three types of maintenance work, desilting and bottom sediment removal had the largest negative impact, significantly reducing taxonomic composition (by an average of 53%), density (by an average of 43%), and ecological index values (by an average of 40%). Over-frequent maintenance can prevent macroinvertebrate populations from recovering, thus depleting the environment of valuable taxa, including those that provide food for fish and other vertebrates.