Using a natural capital framework to inform improvements to water quality and mitigation of climate change requires robust and spatially explicit ecosystem service data. Yet, for coastal habitats this approach is often constrained by a) sufficient and relevant habitat extent data and b) significant variability in baseline assessments used to quantify and value regulatory habitat services. Here, the European Nature Information System (EUNIS) habitat classification scheme is used to map seven key temperate coastal biotopes (littoral sediment, mat-forming green macroalgae, subtidal sediment, saltmarsh, seagrass, reedbeds and native oyster reefs) within the UK’s Solent European Marine Site (SEMS). We then estimate the capacity of these biotopes to remove nitrogen (N) and phosphorus (P) and carbon (C), alongside monetary values associated with the resulting benefits. Littoral and sublittoral sediments (including those combined with macroalgae) were the largest contributors to total N, P and C removal, reflecting their large biotope area. However, our results also show considerable differences in relative biotope contributions to nutrient removal depending on how they are analysed and delineated over large spatial scales. When considered at a regional catchment level seagrass meadows, saltmarshes and reedbeds all had considerable N, P and C removal potential. Overall, we estimate that SEMS biotopes provide nutrient reductions and avoided climate damages equivalent to UK £1.1 billion, although this could be nearly £10 billion if water-treatment infrastructure costs and high carbon trading prices are utilised. Despite the variability in the final natural capital evaluations, the substantial regulatory value of N, P and C ecosystem services support a strong rational for restoring temperate coastal biotopes.