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Eutrophication and sedimentation are affecting global Marine Protected Area (MPA) ecosystems, such as estuaries, as catchments are developed and sea levels rise. Managers are often faced with short term datasets and modelling evidence with which to undertake management of these complex open systems. Longer term datasets which monitor environmental change can be used to improve understanding of estuary biogeochemistry and the resulting ecological response. In this paper we use the case study of Holes Bay, Poole Harbour to explore how palaeoenvironmental archives can be used to extend the evidence base for sediment, nutrient and ecological management within a coastal MPA.