Since 1990 and in particular, after the implementation of the Water Frame Directive, many positive effects of pro-ecological projects are evident; unfortunately, examples of adverse effects have also been observed. This study aims to indicate how some ill-considered actions, called “pro-ecological”, may lead to habitat degradation and the disappearance of valuable hydrobiont species. Two watercourses, representing the lowland gravel stream and sandy stream type, were selected for the study. Literature indicated that in the past, these watercourses were characterized by an excellent ecological status and the presence of valuable rheophilic fauna and flora. Environmental parameters were recorded, macroinvertebrates and ichthyofauna were sampled and analyzed, and finally, indexes were calculated. The results were compared with literature data. In the course of studies conducted in 2011–2015, drastic habitat deterioration and extensive changes in the species structure of ichthyofauna and aquatic invertebrates were observed. Changes in the Smolnica stream have been caused by the three retention basins constructed in 2000, along the lower and middle course; while in Kiszewko, however, the factor for habitat deterioration was connected with the excessive expansion of the Eurasian beaver (Castor fiber), which created a beaver pond 20 m in width, with impoundment elevations of up to 2 m.