Variability in the Agulhas Current system is dominated by meanders, which constitute cyclonic eddies along the inshore edge of the Current on the southeast coast of South Africa. Few studies have investigated the influence of these meanders on hydrographic variability on the adjacent shelf and slope and to date only a handful have been sampled in situ. This study used available in situ data and GLORYS12v1 model output to investigate the impact of meanders on the distribution of Intermediate waters, namely Red Sea Water (RSW) and Antarctic Intermediate Water (AAIW), as well as mechanisms driving these variations. We focussed on four eddies, sampled in situ during July 1998, April 2010, January–February 2017, and July–August 2017. RSW dominated along the inshore edge of the Agulhas Current in the absence of meanders, but larger proportions of AAIW occurred in the presence of cyclonic eddies. During eddy events, the kinematic steering level was raised above the lower boundary of Intermediate waters, increasing cross-frontal mixing of waters at depths of 800–1800 m. Eddy-induced upwelling of Central and Intermediate waters onto the shelf appeared to be inhibited by bands of strong positive relative vorticity (>0.4 × 10−4 s−1), which likely promoted downwelling conditions inshore of the July 1998, April 2010, and July–August 2017 eddies. Weak positive relative vorticity (<0.2 × 10−4 s−1) inshore of the January–February 2017 eddy was associated with enhanced water mass exchange between the shelf and deeper (>1000 m) ocean. GLORYS12v1 was consistently comparable with satellite and in situ data, and simulated the overall distribution of water masses on the continental shelf and slope despite its inability to reflect the influence of river discharge in nearshore regions during austral summer. The model is thus suitable to investigate the influence of Agulhas Current meanders on the hydrography of South Africa's southeast coast.