Four freshwater eels species (Anguilla spp.) occur in South Africa. From sea to source and back, these facultative catadromous species face multiple-stressors including habitat alteration and deterioration, pollution and migration barriers. Although these eels have social and ecological importance, very little is known about their present distribution and impact of multiple stressors on the wellbeing of populations. Understanding these fishes can contribute to the better use and protection of our water resources, especially in rivers where connectivity is impaired. Existing information demonstrates that river penetration potential of species differs. The giant mottled eel Anguilla marmorata generally does not occur above 750 m a.s.l. while African longfin eel Anguilla mossambica should be distributed throughout river systems up to altitudes of 1650 m a.s.l. In this study, we evaluated the distribution and relative abundance of eels in association with environmental variables in the Sundays, Keiskamma and uMgeni Rivers in South Africa using standard night fyke net efforts. It was hypothesised that the longitudinal distribution of the species would differ between the species and between the systems. A longitudinal survey of survey of the Sundays River (n = 450 fyke net sets) and down the Keiskamma River (n = 73 fyke net sets) confirmed this hypothesis with A. marmorata only being sampled only from the lower reaches of the river while A. mossambica was ubiquitous, occurring from headwater streams to the lower reaches. The uMgeni catchement is heavily regulated and impacted by anthropic activities and it is hypothesised that they are virtually absent from the system. Recent surveys confirmed this hypotheses with only 2 individual A. mossambca caught upstream of the first major dams from a comparable sampling effort. This study has provided evidence that represents the effect of barriers on important river ecosystems in South Africa.