Benthic habitat condition assessments are a requirement under various environmental directives. The Marine Strategy Framework Directive (MSFD), for example, challenges member states in a European sea region to perform comparable assessments of good environmental status and improve coherence of their monitoring programmes by 2020. Currently, North Sea countries operate independent monitoring programmes using nationally defined assessment areas. Lack of an agreed OSPAR or EU scale monitoring method and programme has been identified as a priority science need. This paper proposes a method for the development of a coherent and efficient spatial sampling design for benthic habitats on regional level and gives advice on optimal monitoring effort to get more accurate assessments. We use ecologically relevant assessment areas (strata) across national borders and test spatial sample allocation methods. Furthermore, we investigate the number of samples needed in each stratum to reduce the variance for estimating mean number of taxa and abundance. The stratification needs to take into account the spatial heterogeneity of the entire ecosystem. The total sample effort is optimal when sample allocation takes into account the size and benthic variability within those strata. Change point analysis helps to find a balance between sampling effort and precision of the benthic parameter estimate. A joint sampling design for the North Sea could be generated by combining current efforts, and where needed adapting existing national programmes. This serves a coordinated, region-wide, benthic condition status assessment and strengthens regional cooperation to fulfil multiple monitoring tasks, with a scientifically underpinned common approach.