Facing a generalized increase in water degradation, several programmes have been implemented for protecting and enhancing the water quality and associated wildlife, which rely on ecological indicators to assess the degree of deviation from a pristine state. Here, single (species number, Shannon-Wiener H\', Pielou J\') and multi-metric (Estuarine Fish Assessment Index,
EFAI) community-based ecological quality measures were evaluated in a temperate estuary over an 8-year period (2005-2012), and established their relationships with an anthropogenic pressure index (API). Single metric indices were highly variable and neither concordant amongst themselves nor with the
EFAI. The
EFAI was the only index significantly correlated with the API, indicating that higher ecological quality was associated with lower anthropogenic pressure. Pressure scenarios were related with specific fish community composition, as a result of distinct food web complexity and nursery functioning of the estuary. Results were discussed in the scope of the implementation of water protection programmes.