Natural habitats can be described using an array of variables, but metrics that distil these multiple parameters into a single readily comparable value (e.g. a score) can prove useful for spatio-temporal comparisons as well as decisions concerning environmental resource management. In the lagoon of south-western New Caledonia, multiple habitat variables sampled from seagrass meadows were integrated into a single score for comparison of habitat structure across two spatial scales. Collectively, seagrass meadows scored at 69/100, indicating a ‘fair-to-good’ habitat structure. Spatial variation was evident, however, being greatest at the scale of ‘site’ (0.5–5 km) relative to ‘location’ (tens of kilometres). Key metrics of seagrass area, percentage cover and species identity appeared to drive spatial patterns in habitat structure scores. Although the causes of observed site-scale variation in seagrass structure are untested, differences in wave exposure among sites appear a likely contributing factor. Overall, integrated sampling techniques such as that used herein can provide a convenient way to rapidly compare seagrass habitats, and could be useful as early warning indicators of habitat change in regions where anthropogenic impacts that cause seagrass decline (e.g. eutrophication, sediment released from mining) are of concern.