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Prairie streams are dynamic systems in which habitat patches are sporadically created and lost during extreme hydrological events. The persistence of fish species depends on life-history traits that facilitate their widespread dispersal to recolonize habitats after stochastic extirpation. Artificial barriers are thought to reduce recolonization opportunities and to ultimately displace populations downstream, but the ecological consequences of lost diversity above the barriers are largely unknown. The susceptibility of four prairie fishes to fragmentation and the consequent risk to stream ecosystem processes are described. The selected species exhibit wide tolerances to environmental stressors, represent unique functional feeding guilds, and have different habitat affinities. The ability of each species to access (jumping ability) and successfully traverse (swimming endurance) simulated instream barriers was quantified in the laboratory. Experimental stream complexes were used to isolate the effects of these species on ecosystem structure and function. These replicated single-species experiments were compared with 'no fish' controls to identify the ecological role of each. Small vertical barriers blocked most passage, and with open access all species were unable to traverse relatively short distances against modest water velocities. Stream fragmentation will alter headwater fish assemblage structure and promote the most mobile species. Each species had slightly different effects on the stream ecosystem structure resulting from their different habitat preferences and diets. Without colonization opportunities from neighbouring populations, disturbance events will alter headwater fish assemblages and may degrade the ecosystem structure above barriers. Fragmented riverscapes interact with harsh disturbance regimes to form an ecological ratchet. Systematic species loss above barriers outweighs the opportunity for improvement, suggesting that ecosystem structure may be moving downstream.