Estuarine waterbodies typically support diverse and abundant waterbird communities. However, global environmental degradation as a result of anthropogenic activities is leading to species level changes in biodiversity, with top predators such as piscivorous waterbirds being particularly vulnerable to ecosystem changes. The study aimed to document long-term spatial and temporal patterns of abundance of piscivorous and scavenging waterbirds in the Wilderness Lakes Complex (WLC) in the Garden Route National Park, South Africa, and where possible identify potential causes for observed trends. The abundance of waterbirds on these wetlands was determined biannually from 1992 to 2019, with counts conducted from a boat following a standardised route. Historical waterbird abundance data from the 1980s were also used to describe long-term abundance changes. Eight of the species exhibited seasonal variability in abundance with most, excluding Common Tern Sterna hirundo, being more abundant in winter. Substantial changes occurred in the abundance of several species over the four-decade study period, notably increases in Cape Cormorant Phalacrocorax capensis and Great Crested Grebe Podiceps cristatus, and decreases in Common Tern and Black-necked Grebe Podiceps nigricollis. Long-term abundance trends indicate a combination of declining, increasing, and stable populations. Although some species have undergone contrasting abundance changes on different waterbodies in the WLC the dominant pattern was a similar direction of change on most or all waterbodies and in different seasons. Local reasons for changes probably include loss of sandbanks, changing prey availability, and the absence of recreational disturbance on some waterbodies.Conservation implications: Drivers of changes in the abundances of piscivores are likely to be multifaceted, functioning on multiple spatial and temporal scales, and affecting different species in different ways. Recommended local corrective actions include managing emergent macrophyte encroachment on sandbanks, reducing recreational disturbance, managing processes affecting indigenous fish stocks, and protecting nesting sites.