Small-scale fisheries are important in Laos, where rural people heavily depend upon Mekong River and tributary fish stocks for their livelihoods. Increasing pressures from human exploitation and habitat disturbance, however, have raised serious concerns about the potential depletion of various species. This has led to the establishment of large numbers of Fish Conservation Zones (FCZs) or "no-take" fish sanctuaries in southern Laos based on a "community-based fisheries co-management" framework. This study uses the local ecological knowledge (LEK) of fishers to assess the effectiveness of village-managed FCZs in enhancing fish stocks in the mainstream Mekong River in Khong District, Champasak Province. Focus group interviews about species that are believed to have benefited from different FCZs are compared with parameters such as FCZ area, age, depth, localized gradient, water velocity, and the presence of wetland forests nearby. The results suggest that no one aspect is likely to account for variations in fish stocks; rather, it is the interaction between numerous factors that has the largest impact. Secondly, the results indicate that microhabitat diversity and protection are critical for maintaining and enhancing Mekong fisheries. Deep-water pools are particularly important as dry season refuges for many fish species, and FCZ depth may be the single most important environmental factor affecting the success of FCZs in the Mekong River. FCZs have the most potential to benefit relatively sedentary species, but may also benefit highly migratory species, given the right conditions. This study shows that integrated approaches to stock assessment that employ LEK and scientific fisheries management have considerable potential for improving Mekong capture-fisheries management.