The Benthic Ecosystem Quality Index 2 (BEQI2) is the Dutch multi-metric index (MMI) for assessing the status and trend of benthic invertebrates in transitional and coastal waters for the Water Framework Directive (WFD). It contains the same indicators, i.e. species richness, Shannon index and AMBI, as in the multivariate m-AMBI. The latter MMI has been adopted by several European countries in the context of WFD implementation. In contrast to m-AMBI, the BEQI2 calculation procedure has been strongly simplified and consists of two steps, i.e. the separate indicator values are normalized using their long-term reference values resulting in three Ecological Quality Ratios (EQRs), which are subsequently averaged to give one BEQI2 value. Using this method only small numbers of samples need to be analysed by Dutch benthos laboratories annually, without the necessity to co-analyse a larger historical dataset. BEQI2 EQR values appeared to correlate quantitatively very well with m-AMBI EQR values. In addition, a data pooling procedure has been added to the BEQI2 tool which enables the pooling of small core samples (0.01–0.025 m2) into larger standardized data pools of 0.1 m2 in order to meet the data requirements of the AMBI indicator and to obtain comparable reference values. Furthermore, the BEQI2 tool automatically and efficiently converts species synonym names into standardized species names. The BEQI2 tool has been applied to all Dutch benthos data monitored by Rijkswaterstaat in the period of 1991–2010 in the transitional and coastal waters and salt lakes and these results are reported here for the first time. Reference values for species richness and Shannon index (99 percentile values) and AMBI reference values (1 percentile values) were estimated for all water body–ecotopes and are discussed. BEQI2 results for all these water bodies are discussed in view of natural and human pressures. The pressure sensitivity of the BEQI2 for sewage and dredging/dumping, via the state variables oxygen and suspended matter respectively, was demonstrated.