The spatialisation of essential biodiversity variables is a crucial step in assessing the health of coral reefs. However, few studies propose a comprehensive method for a large-scale assessment, such as coral reefs around Reunion Island. This requires a trade-off between the area, the study time, and the number of sampled stations needed to achieve spatial interpolations at an acceptable human and financial cost. We estimated nine sighting benthic biodiversity variables through visual assessments conducted in 2,599 circular plots per 100 m², distributed in two zones (reef flat, outer slope) and 14 habitats present across four sites (fringing reefs) on Reunion Island. A stratified sampling plan that is homogeneous within zones and differentiate between zones is appropriate, particularly for the study of a reef at several spatial scales (site, zone, habitat). We first demonstrated that the sampling effort enabled statistical discrimination and spatialisation of the nine benthic biodiversity variables within all the landscape units. Subsequently, we investigated the reliability limits of the spatial models by reducing the sampling effort of an increasing proportion of stations using bootstrap resampling. Results showed that station densities of 0.5 to 1.2 stations.ha− 1 (outer slopes) and 1.5 to 4.3 stations.ha− 1 (reef flats) provide very satisfactory to excellent spatialisation of the essential biodiversity variables. Depending on the objectives, the resolution and the available resources, our method allows an estimation of the trade-off between required information for mapping benthic biodiversity variables of coral reefs using spatial interpolation and sampling effort.