The objective of this study was to use an integrative approach to assess the ecological status of a small river impacted by multiple sources of disturbance. The River Febros (NW Portugal) is a small and highly impacted non-regulated river; approximately 44% of the watershed area is dedicated to agriculture, but there is also some urbanization. Environmental status was evaluated using a new multi-index approach, combining quality indices for water (Water Quality Index (WQI)), benthic macroinvertebrates (Iberian Biological Monitoring Working Party Index (IBMWP)), and human modification (Riparian Forest Quality Index (QBR)); Ecological Status River Mediterranean Index (ECOSTRIMED); River Habitat Survey (RHS)). Surveys were carried out between October 2002 and 2003, along four stretches of the main course of the river for physicochemical characteristics, as well as water microbiology and macroinvertebrates. Water quality was poor at all sites (WQI averaged 30.4%) and decreased downstream. The RHS (assessment of instream habitats and the river corridor) and the QBR quantification displayed the same trend. Macroinvertebrates diversity was permanently low with only the most tolerant insects taxa present; oligochaetes dominated. The ecological status of River Febros was well represented using the experimental assessment system, where a downstream decrease in condition was noticeable (in spite of a lower water quality upstream). Our results emphasize the importance of assessing several components of disturbed ecosystems in order to ascertain overall quality and the importance of promoting improvement of the riparian gallery as a buffer against multiple agents of disturbance.