The coexistence of trees and grasses in savanna ecosystems is a contentious phenomenon. Fire and herbivory disturbances are often cited as major structuring forces that create a sustainable tree–grass relationship. However, periodic flooding of savanna patches may also enable coexistence. The aim of this study was to investigate the effects of flood-disturbance on the recruitment patterns of Acacia karroo trees in a semi-arid savanna system in South Africa. We analysed the spatial coincidence of A. karroo seedlings with tussocks of the tall spiny grass Stipagrostis namaquensis in the riverbed and related herbivory intensity to spatial position. The data showed that A. karroo seedlings were significantly positively associated with S. namaquensis (Chi-square test, χ21=45.20χ12=45.20, n = 118, P < 0.001); A. karroo seedlings growing inside of tussocks experienced less browsing pressure than those growing in the floodplain (Kruskal–Wallis test, H = 11.90, n = 118, P < 0.01); and recruitment success of A. karroo trees was spatially discrete (K–S test, D = 0.78, n = 196, P < 0.01). We suggest that floods create an enemy-free zone, which S. namaquensis colonises and then facilitates successful A. karroo establishment. High levels of A. karroo recruitment in the riverbed may replenish the woodlands fringing the river, which appear to be sink areas for A. karroo seedlings. Thus, the interaction between disturbances at different spatial and temporal scales (flooding versus herbivory) seems to maintain the inherently unstable coexistence of tree and grass species in this ecosystem. These findings also suggested that flood disturbances alter the tree–grass relationship. Keywords: Savanna dynamics, tree-grass coexistence, flood disturbance, Herbivory, facilitation, recruitment, patch dynamics.