People throughout the world depend on the services we derive from freshwater ecosystems. Human land-use activities often affect the quality, quantity and habitat of freshwater ecosystem, which need to be carefully managed to ensure their integrity and provision of services is sustainable. In South Africa, legislation has established resource-directed measures to attain a sustainable balance between the use and protection of water resources. These procedures have been implemented in most of South Africa’s nine water-management areas, resulting in new legislation to protect these resources. Unfortunately, very little protection has been afforded to river connectivity maintenance and fish migrations. For water storage and flow regulation for agriculture and other resource use activities, >610 formal dams and ~1430 gauging weirs have been constructed that act a partial or complete barriers to fish migration on river ecosystems. Only ~60 fish passage structures have been built, but many are not functional. River connectivity and fish migration management appears to be a shortcoming of the existing management approach for multiple stressors.

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Context In developing countries, fish data might be lacking and expensive to collect. Fisher’s local ecological knowledge (LEK) has been identified as important to complement scientific data gaps. However, consensus and divergences between both methods have not been extensively studied. Aims This paper compares local fishers’ LEK and scientifically sampled data on fish species composition, ecological preferences, and wellbeing in the Lower Komati River, South Africa. Methods Key informant interviews (n = 6), field tracking (n = 5) and participatory mapping (n = 22) were undertaken to capture fishers’ LEK and produce maps showing fishing points. Two science-led fish surveys in six sites were also undertaken between August 2019 and December 2019 by using an electrofishing method. Key results The fishers’ LEK and survey data showed similar patterns of occurrence of Micralestes acutidens, Coptodon rendalli, Oreochromis mossambicus and Labeo cylindricus. Comparing fishers’ catch estimates and survey catch showed that there is no significant difference (P > 0.05) in abundance on the two most sampled species by using ANOVA. Conclusion Differences between the two methods were observed in assessing the river and fish’s wellbeing. Implication The similarities and differences were identified as opportunities for small-scale fisheries and scientists to co-identify ecosystem management strategies that are congruent to the local environment.

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