The combination of intensive agricultural activities and the close connectivity between land and stream emphasise the potential risk of pesticide exposure in Danish streams. Benthic macroinvertebrates are applied in the assessment of stream ecological status, and some sensitive species have been shown to respond strongly to brief pulses of pesticide contamination. In this study we investigate the impact of agriculturally derived pesticides on stream macroinvertebrate communities in Denmark. As a measure of toxic pressure we apply the Runoff Potential. We investigated a total of 212 streams. These were grouped into distinct classes according to the magnitude of pesticide contamination in the period from 2003-2006. A total of 24 different macroinvertebrate indices were applied to detect effects of pesticide runoff (e.g. the SPEAR-index and the number of EPT taxa). We found high predicted pesticide runoff in 39% of the streams, but we found no significant effect of predicted pesticide exposure on stream macroinvertebrate indices. We, additionally, examined the influence of a series of environmental parameters ranging from site scale to catchment scale on the macroinvertebrate community. Relative proportions of gravel, sand and silt in bed sediments explained most of the variation in macroinvertebrate indices as well as the upstream riparian habitat quality. We suggest that the Runoff Potential model overestimate pesticide runoff contamination in Danish streams due the presence of buffer strips enforced by Danish legislation. When pesticide runoff contamination is low to moderate, poor physical properties (indirectly related to agricultural activity) are the main impediment for the ecological quality of Danish streams.