A wide array of pesticides are applied to agricultural crops during spring and autumn spraying season, and detections of pesticides in stream water and bed sediments of agricultural streams emphasize the potential exposure of benthic macroinvertebrates. Major transportation routes from catchment to stream are surface runoff and tile drainage giving rise to short pulses of acute contamination strongly coinciding with high levels of precipitation. Field studies indicate that macroinvertebrate community structure can be impacted by pesticides during spraying seasons in May and June, but also that it is difficult to disentangle the specific effects of pesticides from those related to the poor physical conditions prevailing in the majority of agricultural streams. This study aims to separate the effects of pesticides from those of poor physical conditions. Model based predicted pesticide loss to streams was calculated for 1 km2 catchments (produced from topographical maps) on Funen, Denmark. The physical condition (substrate, meandering etc.) of 1st and 2nd order streams (based on existing data from the National Monitoring Programme and personal exploring) draining these catchments was, additionally, assessed. Subsequently, 15 small streams were selected representing different expected pesticide loading. In each stream two successive reaches differing in physical properties (upstream reach characterised by poor and downstream by good physical conditions) was selected. In spring 2009 the pesticide concentrations in each stream were measured applying sediment sampling and event triggered water samplers. Furthermore, on all reaches macroinvertebrate community structure was assessed before, during and after the spring application season. Stream reaches with good physical quality generally contain a higher abundance and species richness of EPT taxa and we therefore hypothesize that reaches with good physical properties are more sensitive to acute pesticide contamination (measured as the frequency of SPEcies At Risk) than reaches with poor physical properties.