We analyze the influence of surface heterogeneity, inducing a random-potential at the walls in electroosmotic incompressible flows. Specifically, we focus on how surface heterogeneity modifies the physico-chemical processes (transport, chemical reaction, mixing) occurring in microchannel and microreactors. While the macroscopic short-time features associated with solute transport (e.g. chromatographic patterns) do not depend significantly on zeta-potential heterogeneity, spatial randomness in the surface zeta-potential modifies the spectral properties of the advection diffusion operator, determining different long-term properties of transport/reaction phenomena compared to the homogeneous case. Examples of physical relevance (chromatography, infinitely fast reactions) are addressed. (c) 2007 Elsevier B.V. All rights reserved.