Quantifying the uncertainty associated with monitoring protocols is essential to prevent the misclassification of ecological status and to improve sampling design. We assessed the Posidonia oceanica multivariate index (POMI) bio-monitoring program for its robustness in classifying the ecological status of coastal waters within the Water Framework Directive. We used a 7-year data set covering 30 sites along 500 km of the Catalonian coastline to examine which version of POMI (14 or 9 metrics) maximises precision in classifying the ecological status of meadows. Five factors (zones within a site, sites within a water body, depth, years and surveyors) that potentially generate classification uncertainty were examined in detail. Of these, depth was a major source of uncertainty, while all the remaining spatial and temporal factors displayed low variability. POMI 9 matched POMI 14 in all factors, and could effectively replace it in future monitoring programs.