Abstract. Pumping of neutral gas and re-fuelling in other locations (e.g. neutral beam injection, gas puffing) is a key ingredient in divertor physics. However, this has not been included in previous 3D edge plasma transport simulations with the EMC3-EIRENE code. Including these effects brings the simulations closer to reality and we demonstrate that this has a significant impact on divertor parameters. In particular, we study the impact of the pumping efficiency on ITER similar shape plasmas at the DIII-D tokamak in the presence of resonant magnetic perturbations (RMPs). Further, we investigate the so called "particle pump-out effect". We show that in the present transport model and for given pumping and re-fuelling rates, the density at the transition to the core region decreases with increasing perturbation current, but the temperature as well. The striation patterns in the target particle and heat fluxes are extended into the regular SOL, which is caused by cross-field transport into a thin layer around the perturbed separatrix.