We studied the performance of the AZTI Marine Biotic Index AMBI manipulating input data collected from lagoonal ecosystems. Our data set consisted of macrofaunal abundance and biomass counts gathered at a variety of sites at which the disturbance status was known. Input data were also manipulated using a set of transformations of increasing severity. Biotic indices were calculated using raw and transformed abundance, biomass and production. Among the three categories of AMBI-based indices, medium transformation of data gave the highest correlation with pressures. However, increasing the severity of transformation generally resulted in a decrease of the correlation with environmental factors. The relative importance of ecological groups changed when using abundance or biomass, sometimes leading to an improved ecological status classification. Being biomass and production more ecologically relevant than abundance, using them to derive AMBI-based new indices seems intriguing, at least in lagoonal waters, where the community is naturally disturbed and dominated by opportunists.