Historically, ecological engineered solutions for fish passage across anthropogenic barriers in rivers has mainly focused on facilitating upstream passage for long-migrating diadromous fish, such as salmonids. More recently, passage solutions have shifted their focus to a more holistic ecological perspective, allowing passage for species with different swimming capacity, both upstream and downstream. This experiment investigated whether the addition of cobble in the passageway of a surface bypass could facilitate downstream movement of a cyprinid fish, the common roach Rutilus rutilus. Surface bypasses were constructed in large experimental flumes and roach were released into the flumes and monitored for bypass passage using PIT-telemetry through 11-h night-trials. Behavior was scored using four continuously-recording video cameras at the bypass construction. There was a negative effect of substrate-treatment on the passage rate through the bypass. The majority of the fish in the No substrate treatment had successfully passed within 4 h, while a lesser proportion of the fish in the Substrate treatment had done so (additional fish in the latter treatment passed later in the trials). Fish exposed to cobble substrate in the bypass passageway showed more avoidance-like behaviors at the ramp section of the bypass and tended to return back upstream more often than the fish in the no-substrate control trials. When reaching the passageway, the substrate-exposed fish expressed no behaviors that could be indicative of reduced passage success, as compared to controls. We conclude that passage was not hindered by the presence of cobble substrate, but passage was delayed due to avoidance behavior at the bypass ramp when cobble substrate was present. Based on these results, the addition of cobble substrate in a surface bypass cannot be recommended as a measure to facilitate the downstream passage performance of the common roach through surface bypasses.