Bioindicators are essential for detecting environmental degradation and for assessing the success of river restoration initiatives. River restoration projects require the identification of environmental and pressure gradients that affect the river system under study and the selection of suitable indicators to assess habitat quality before, during and after restoration. We assessed the response of benthic macroinvertebrates, fish, bird and macrophyte assemblages to environmental and pressure gradients from sites situated upstream and downstream of a cofferdam on the River Odelouca, an intermittent Mediterranean river in southwest Portugal. The Odelouca will be permanently dammed in 2010. Principal Component Analyses (PCA) of environmental and pressure variables revealed that most variance was explained by environmental factors that clearly separated sites upstream and downstream of the partially built cofferdam. The pressure gradient describing physical impacts to the banks and channel as a result of land use change was less distinct. Redundancy Analysis revealed significant levels of explained variance to species distribution patterns in relation to environmental and pressure variables for all 4 biological assemblages. Partial Redundancy analyses revealed high levels of redundancy for pH between groups and that the avifauna was best associated with pressures acting upon the system. Patterns in invertebrates and fish were associated with descriptors of habitat quality, although fish distribution patterns were affected by reduced connectivity. Procrustean and RELATE (Mantel test) analyses gave broadly similar results and supported these findings. We give suggestions on the suitability of key indicator groups such as benthic macroinvertebrates and endemic fish species to assess in stream habitat quality and appropriate restoration measures, such as the release of peak flow patterns that mimic intermittent Mediterranean systems to combat habitat fragmentation and reduced connectivity.