Cross-barriers such as small dams cause local flow velocity heterogeneities, which might affect the formation, structure, and function of biofilms. The main objective of this thesis was to investigate the impact of flow velocity on colonization dynamics, grazing activity, and behavioral changes of biofilm associated ciliates. In addition, the effect of protists grazing activity on spatial biofilm morphology was examined at slow flow velocities. Surfaces were rapidly colonized by ciliates at a slow flowing reservoir of the third order Ilm stream (Thuringia, Germany) and in slow flowing flow channels. Initial stream biofilms inhabited all functional groups of ciliates irrespective of flow velocity implementing all trophic links within the microbial loop. The low abundance of sessile filter feeders at faster flow velocities suggested that the attachment of these cells was inhibited. Grazing activity of a previously attached filter feeder seemed to be inhibited at faster flow velocities since cells remained about 45% of the observed time in a contracted state. Vagile flattened gulper feeder tolerated faster flow velocities and responded with a positive rheotactic movement. Grazing activity and motility of ciliates altered spatial biofilm morphology. Mushroom shaped microcolonies, a higher porosity, and a higher biofilm surface area to volume ratio indicated that nutrient exchange between biofilm and the surrounding fluid was improved and bacterial growth might be accelerated. With respect to restoration ecology the data indicated that flow velocity differences at small low-head dams increased the diversity of biofilm associated ciliates, which might contribute to enhanced ecosystem resilience.