Invasive, non-indigenous plants such as marram grass (Ammophila arenaria) have been used extensively in New Zealand to stabilise dune systems but this activity has resulted in a loss of indigenous biodiversity as well as significant changes in dune morphology. The restoration of natural dune systems has become a focus for some of the least modified coastal regions with associated concerns as to what effect marram grass eradication or other such interventions may have on dune stability.An ongoing project at Mason Bay, Stewart Island, New Zealand has examined all aspects of marram grass invasion and eradication. This paper concentrates on the initial three-dimensional CFD model that simulates the wind flow over this complex dune system compared with field data with detailed LIDAR data used to recreate the complex topography of the dune system. Various modelling options are assessed for their accuracy in emulating the field data. The topography was found to greatly affect the results, making it difficult to determine the actual wind flow pattern over such a complex system. The effectiveness of three-versus two-dimensional CFD modelling is therefore discussed in terms of accuracy, practicality and complexity and the feasibility for practical planning purposes is also explored.