The aspirations for natural capital and ecosystem service approaches to support environmental decision-making have not been fully realised in terms of their actual application in policy and management contexts. Application of the natural capital approach requires a range of methods, which as yet have not been fully tested in the context of decision making for the marine environment. It is unlikely that existing methodologies, which were developed for terrestrial systems and are based on land cover assessment approaches, will ever be feasible in the marine context at the national scale. Land cover approaches are also fundamentally insufficient for the marine environment because they do not take account of the water column, the significant interconnections between spatially disparate components, or the highly dynamic nature of the marine ecosystem, for example the high spatial mobility of many species. Data gaps have been a significant impediment to progress, so alternative methods that use proxies for quality information as well as the opportunities for remote sensing should be explored further. Greater effort to develop methodologies specifically for the marine environment is required, which should be interdisciplinary and cross-sectoral, coherent across policy areas, and applicable across a range of contexts.