Despite the requirements of the European Water Framework Directive (WFD) to protect water bodies, suitable indices of quality designed specifically to assess coastal lagoons (transitional waters) remain absent. In the present study, we developed a multimetric index of the Balearic Island based on invertebrate communities (MIBIIN) to assess the ecological status of small coastal lagoons (i.e. up to 4-m depth and ,2.5 km2), a common ecosystem within the Mediterranean ecoregion. Thirty-four coastal lagoons were sampled on six occasions between 2005 and 2008. A multimetric index for each salinity type of coastal lagoon (oligohaline-MIBIIN, mesohaline-MIBIIN and euhaline-MIBIIN) was developed. The individual metrics, and hence the MIBIINs, fulfilled the normative definitions established by the WFD (abundance, diversity and sensitive : tolerance ratio), responded to gradients of disturbance and discriminated reference from non-reference sites. Common boundary limits for the three MIBIINs were established (high/goodÂ¼0.930, good/moderateÂ¼0.730, moderate/poorÂ¼0.500, poor/badÂ¼0.250). Unlike other metrics used in coastal lagoon evaluation, the MIBIINs were developed exclusively for coastal lagoons, including oligohaline freshwater environments. Although the MIBIIN is yet to be validated with an external dataset, these findings suggest the potential for this new multimetric index to be used in similar systems in the Mediterranean ecoregion.