Globally, many shorebirds, particularly the smaller migratory waders are declining, which can be attributed to multiple factors throughout their ranges. The Wilderness Lakes Complex in South Africa comprises two estuarine systems, that support diverse waterbird communities, including 17 abundant shorebirds. The study aimed to document long-term spatial and temporal patterns of abundance of shorebirds in the Wilderness Lakes Complex, 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 abundance data from the 1980s were also used to describe long-term abundance changes. Ten shorebirds showed seasonal differences in abundances. Significant long-term decreases in abundance have occurred in seven shorebirds (Wood Sandpiper Tringa glareola, Marsh Sandpiper Tringa stagnatilis, Curlew Sandpiper Calidris ferruginea, Ruff Philomachus pugnax, Grey Heron Ardea cinerea, Greater Flamingo Phoenicopterus ruber, Black-winged Stilt Himantopus himantopus) and increases in three species (African Spoonbill Platalea alba, Little Egret Egretta garzetta, Glossy Ibis Plegadis falcinellus). Similar types of population changes occurred across multiple waterbodies and in different seasons. The similarity of shorebird abundance trends in spatially separated wetlands suggests either high interconnectivity of populations between wetlands systems and/or prominent drivers of change being broad scaled rather than system specific. Local reasons for changes potentially include the increasing spread of emergent macrophytes and resultant loss of open sandbanks, changing hydrodynamics, and alien fish proliferation, all likely changing food accessibility, as well as periodic high disturbance by waterbody users.Conservation implications: Changes in the abundances of several shorebirds, particularly small migratory waders, are substantial, with multiple likely local, regional and international drivers acting accumulatively. Recommended corrective actions include continuing involvement in the development and implementation of policies for waterbird conservation, and local management of emergent macrophytes, disturbance, and water level variability.