Connectivity between river-floodplain habitats has been heavily constrained in many large tropical river systems by the construction of regulators, levees and other physical barriers. Fishways are being constructed to ameliorate the effects of these barriers; but it is important that all aspects of fishway design cater for local target species. We investigated the lateral movement patterns of Lower Mekong Basin fish in Laos, through a fishway that incorporated a series of cones, resting pools, and a culvert with a vertical lift gate. Fish needed to negotiate all of these structures to move from the Mekong to an adjacent wetland. We tested the hypothesis that gated culverts may hamper the effectiveness of fishways, by comparing the abundance and species richness of fish at three locations along the path of the fishway and culvert: (1) the fishway entrance; (2) the fishway exit; and (3) the culvert exit (i.e. immediately upstream of the culvert). There were no marked differences in the total abundance and species richness of fish between the fishway entrance and culvert exit while the river remained at levels where the culvert was only partially inundated. Nevertheless, the abundance and species richness of fish were markedly lower at the culvert exit than at the fishway entrance and exit once the headwater levels rose to where the culvert was completely inundated. These findings indicate that fish were able to ascend the fishway but not the culvert once it became completely submerged, and thus support the hypothesis that gated culverts can hamper the effectiveness of fishways in facilitating the lateral movement of fish in large tropical systems. Fish passage at such installations can be enhanced through optimised operating regimes. Ensuring that headwater levels remain below the culvert ceiling is likely to be the best way to maximise fishway effectiveness.