The Spanish National Advisory Board of Mariculture (JACUMAR) developed an initiative to unify methodologies between the regions of Spain, in which they proposed the implementation of site-specific “Environmental Monitoring Plans” (EMPs). In this study, we tested the feasibility of an EMP on a fish farm in the Mediterranean Sea. The methods and tools proposed in the EMP are highly useful for environmental monitoring of aquaculture. However, spatial heterogeneity figured prominently in a univariate analysis with environmental variables and a multivariate analysis of polychaete assemblages. This variability may be due to habitat patchiness, and may therefore be solved by an improved experimental design, e.g. by adding replications for increasing statistical power. Multivariate analysis of polychaete assemblages provided accurate information about the quality of the sediment. This information could also be improved using ecological data about key polychaete families in order to avoid misleading results. Thus, the JACUMAR EMP has proved useful in providing precise information about the ecological status of marine benthic habitats, meeting the requirements of current European Directives. However, we suggest that some modifications may be required in order to account for possible misleading thresholds for environmental quality standards, spatial heterogeneity and increasing power analyses.