## 2 Materials and Methods
### Validation of the Method with Ecological Status Metrics  
The results of the pressure levels assessed with the proposed method, were correlated with the available public data on the ecological status assessment by using the indicators (metrics) available in European databases [35] and the River Basin Authorities database (Table S2). Data for the Mediterranean coastal lagoons were obtained from available datasets in the European Environmental Agency resources [35]. The information used corresponds to the databases: _\"Waterbase_--Lakes\" (which included the data for CABR, GELA and ALBU sites, freshwater to brackish lagoons) and _\"Waterbase_--Transitional, coastal and marine waters\" (which included the brackish and saline lagoons). These data were obtained from disaggregated databases. Not all the lagoons had available information on every metrics studied. The physical and chemical variables (indicators) selected included concentrations of ammonium (\(\mu\)mol N L\({}^{-1}\)), dissolved oxygen (\(\mu\)M O\({}_{2}\) L\({}^{-1}\)), nitrate (\(\mu\)M N L\({}^{-1}\)), nitrite (\(\mu\)M N L\({}^{-1}\)), orthophosphate (\(\mu\)mol P L\({}^{-1}\)), silica (\(\mu\)M Si L\({}^{-1}\)), total nitrogen (\(\mu\)M N L\({}^{-1}\)), and total phosphorus (\(\mu\)M P L\({}^{-1}\)), although for some of them there were not enough data for a proper statistical analysis. The data sources and availability for these selected variables in the studied lagoons are shown in Tables S2 and S3. As biological indicators, three main biological quality elements (BQE), described in the WFD, were selected. Phytoplankton abundance was used as a measure of the chlorophyll-\(a\) concentration (chl-\(a\), \(\mu\)g L\({}^{-1}\)); this, as well as the macrophytes coverage and benthic fauna, were in all cases normalized as the Ecological Quality Ratios (EQR) (ranking between 0 to 1, dividing classifications between bad, poor, moderate, good and high status). In terms of both macrophyte coverage and benthic fauna, little or no information was present in the European databases for the selected coastal lagoons. Therefore, these data were obtained from national reports on the ecological status of these waterbodies, according to the WFD, available from River Basin Authorities of Spain and France. Macrophyte BQE assessment for both member states was mainly based on the percentage of vegetation cover, the relative percentage of type-specific taxa, and the specific richness. Indices used for the benthic fauna in France were AMBI (AZTI Marine Biotic Index) and multivariate-AMBI (M-AMBI). AMBI is based on the relative abundance of the species of the benthic macrofauna classified in ecological groups, which represent different degrees of tolerance to the alteration of the environment. AMBI correlates with an anthropogenic index, in this case the % of organic matter in sediments (as indicated in the national reports included in Table S2). M-AMBI is obtained by factor analysis, from the AMBI, the specific richness S and the diversity index H\({}^{\prime}\). In Spain, the standardized benthic invertebrates index used for lenti waterbodies is the IBCAEL, that joins two indices assessing the taxonomic composition and the abundance of the benthic invertebrate assemblages. This index has also previously been demonstrated to be a good indicator of the ecological quality of lenti waterbodies [53]. References to the reports and websites from where the information was obtained, as well as to the protocols of the sampling and index determination, can be found in Table S2. The results of the LUPLES method for quantifying the pressures of eutrophication, organic enrichment, acidification and toxic pollution in each coastal lagoon were correlated with the values of the quality indicators of the ecological status, to validate the method and determine the correlations. Each pressure level assessed, corresponding to each study site, was correlated with the available physical-chemical and biological disaggregated metric data.