A procedure to select the most relevant metrics for assessing the ecological condition of the Douro basin (north Portugal) was developed based upon a set of 184 benthic community metrics. They were grouped into 16 biological categories selected from literature using data collected over 2 years from 54 sites along 31 rivers covering the whole perceived range of human disturbance. Multivariate analyses were carried out to identify the main trends in the macroinvertebrate data, to select reference versus impaired sites, to avoid multicolinearity between metrics, and to identify those that were clearly independent from natural stream typology. Structural metrics, adaptation metrics, and tolerance measures most effectively responded across a range of human influence. We find these attributes to be ecologically sound for monitoring Portugal's lotic ecosystems and providing information relevant to the Water Framework Directive, which asserts that the definition of water quality depends on its "ecological status", independent of the actual or potential uses of those waters.