The initial rate of colloid deposition onto semi-permeable membranes is largely controlled by the coupled influence of permeation drag and particle-membrane colloidal interactions. Recent studies show that the particle-membrane interactions are subject to immense local variations due to the inherent morphological heterogeneity (roughness) of reverse osmosis (RO) and nanofiltration (NF) membranes. This experimental investigation reports the effect of membrane roughness on the initial deposition of polystyrene latex particles on a rough NF membrane during cross flow membrane filtration under different operating pressures and solution chemistries. Atomic force microscopy was used to characterize the roughness of the membrane and observe the structure of particle deposits. At the initial stages of fouling, the AFM images show that more particles preferentially accumulate near the "peaks" than in the "valleys" of the rough NF membrane surface.