In water limited systems vegetation self-organises into a mosaic of vegetated patches and bare soil. Long range competition (C) for water and short range facilitation (F) are a known mechanism for vegetation pattern formation. A topographic gradient allows patches interact via interception of surface runoff, but little is known about the self-organisation of vegetation patchiness when topography is not smooth. Here we show, with a C-F cellular automata model, that variation in topography, controlling surface water redistribution, can significantly alter self-organised vegetation patterns. We reproduce patterns where flow convergence occurs as well as the self organisation of vegetation along an ephemeral fluvial network. These results also suggest that sediment transport processes, smoothing the terrain, are essential for the maintenance of banded patterns.