Abstract The essential biodiversity variables (EBV) framework was developed primarily to improve the detection of significant changes in global biodiversity. Its application at national level must support county-specific policy and management needs as well as allowing comparisons of estimates of biodiversity change between countries and their aggregation for reporting at regional, continental and global scales. Here we outline a process for prioritising biodiversity variables at national scale using the EBV framework. The process involves separately identifying candidate EBVs that are useful for tracking important changes in biodiversity in each major ecological feature in each ecoregion within a country. The list is then prioritised based on the proportion of ecological feature ecoregion combinations using each variable within and across terrestrial, marine and freshwater realms. We showcased this process in Australian state of New South Wales (NSW) using terrestrial, marine and freshwater ecoregions of the world as bioregional strata; vegetation formations as terrestrial ecological features, and broad aquatic ecosystem types as marine and freshwater ecological features. There was sufficient knowledge of ecological processes to identify useful variables for 85% of the ecological feature ecoregion combinations in NSW. Eleven candidate EBVs covering all six EBV classes, were useful in all three environmental realms. Our structured, stepwise approach to variable selection provides a transparent process for identifying important elements of ecological theory underpinning biodiversity monitoring within countries. Worldwide adoption of a process for prioritising biodiversity variables such as the one we propose here would help ensure consistency of national contributions to global biodiversity assessments.