In Europe, the routes of most watercourses were straightened and shortened, leading to the destruction and degradation of many natural environments. Currently, in places where it is possible, as part of the implementation of the Water Framework Directive, efforts are made to improve environmental sustainability, including improving the ecological condition of rivers. This paper presents the impact of three in-stream deflectors on changes in the section of a small lowland river—the Flinta (Poland)—where (from 2018 to 2023) detailed, systematic geodetic, and hydrometric research and an assessment of the ecological conditions were carried out. The presented results show the influence of deflectors on the initiation of fluvial processes in the transverse and longitudinal layouts of the channel. The river channel was narrowed from 6 to 5 m, and the current line shifted by almost 3 m. Changes were observed in the distribution of velocities and shear stresses, varying along the surveyed section of the river. In the first year after their application, an increase in velocity at the deflectors can be observed (from 0.2 m∙s−1 to 0.6 m∙s−1 in the deflector cross-section). In the following years, on the other hand, a clear decrease in velocity was observed in the sections between the deflectors (to 0.3 m∙s−1). The introduction of deflectors resulted in a significant increase in the values of shear stresses (from an average value of 0.0241 N∙m−2 in 2018 to 0.2761 N∙m−2 in 2023) and local roughness coefficients (from 0.045 s∙m−1/3 before the introduction of the deflectors to 0.070 s∙m−1/3 in 2023). Based on analyses of sediment samples, erosion and accumulation of bottom material were initially observed, followed by a subsequent stabilisation of particle size. Differences in grain size were observed, especially in the cross-section of the deflectors (increase in granularity d50% downstream of the deflector from 0.31 mm to 3.9 mm already 2 years after the introduction of deflectors). This study confirmed the positive impact of using deflectors on hydromorphological processes as deflectors facilitate the achievement of a good ecological status, as required by the WFD. The innovation of this paper lies in demonstrating the possibility of using small, simple structures to initiate and intensify fluvial processes, which may contribute to improving the ecological conditions of watercourses.