Hidden in intertidal sandflats of our estuaries live shellfish, worms, and crabs. We are interested in defining how the relationships between their abundance patterns and different biotic and environmental processes change from single points to across whole intertidal areas. We will determine the importance of environmental characteristics within and across spatial scales and assess their interaction with biological processes. This will be achieved by employing spatially explicit Generalised Estimating Equations within spatial scales, and multivariate spatial Bayesian models that include species interactions as well as environmental variability across spatial scales. Thereby we will be able to better understand the interplay between fine- and broad-scale patterns and processes that underpins potential resilience in these ecosystems and improve our forecast of habitat preferences under conditions of environmental change. To date, most broad-scale research on species distributions ignores spatial patterns, scale-dependent variability, and biotic interactions. This limits our statistical analyses and more importantly inferences about ecological processes we draw from them. We will will visit more than 1000 strategically positioned sampling stations in three of New Zealand’s major harbours. Predicting current and potential distributions of species is critical for evaluating management options and understanding the importance of ecological change, leading towards a better integrated management of coastal ecosystems. This is fundamentally important due to catastrophic global shifts in many marine ecosystems, following over-harvesting, pollution, and the direct and indirect impacts of climate change. This integrated and holistic approach can only be realised by pulling together an unrivalled knowledge of estuarine ecosystems, provided by the National Institute for Water & Atmospheric Research, and a fully equipped toolbox, contributed by the University of Freiburg.