Agricultural intensification during the last century has caused river degradation across Europe. From the wide range of stressors derived from agricultural activities that impact rivers, diffuse agricultural pollution has received most of the attention from managers and scientists. The aim of this study was to determine the main stressors exerted by intensive agriculture on streams around Nitrate Vulnerable Zones (NVZs), which are areas of land that drain into waters polluted by nitrates according to the European Nitrate Directive (91/676/EEC). The study area was located in the NW of La Rioja (Northern Spain), which has some of the highest nitrate concentrations within the Ebro basin. The relationships between 40 environmental variables and the taxonomic and functional characteristics of the macroinvertebrate assemblages (which are useful indicators of water quality) were analyzed in 11 stream reaches differentially affected by upstream agricultural activity. The streams affected by a greater percentage of agricultural land cover in the surrounding catchment had significantly higher nitrate concentrations than the remaining sites. However, hydromorphological alteration (i.e. channel simplification, riparian forest and habitat degradation), which is closely linked to agricultural practices, was the main factor affecting macroinvertebrate assemblages. We suggest that 'good agricultural practices' should be implemented in streams affected by NVZs to reverse stream degradation, in concordance with the European Water Framework Directive (WFD).