Regulatory risk assessment aims at estimating levels of pesticide use, which are safe for non-target organisms and ecosystem functions. Nevertheless, several studies linked pesticide use to the ongoing biodiversity loss, which is particularly pronounced in freshwater ecosystems. Reported effects span from single species to community levels. This among other might be the reason that a majority of small European freshwater streams exhibit a bad ecological status. These observations suggest that the current approach is not protective for non-target organisms and freshwater ecosystems. An explanation may be that co-occurring stressors, which increase the susceptibility of non-target organisms, are not considered during the risk assessment. To quantify the contribution of pesticides to community changes, declining abundances or changes on ecosystem level, studies with independent gradients of pesticides and additional stressors are required. Suitable study sites are difficult to find in central Europe with its intensive agriculture. Therefore, we conducted a study in Romania, where both extensive agriculture (small fields, mainly hand labor) and highly industrialized agriculture can be found. We sampled 19 stream sites with varying degrees of agricultural land use intensities within their catchments. We assumed that nutrient inputs are uncorrelated to agricultural intensity, as extensive agriculture also uses manure, whereas pesticide inputs mostly originate from industrialized agriculture. We measured pesticide and nutrient concentrations in the water phase as well as several habitat parameters related to the intensity of agricultural land use. Moreover, the ecological status of the streams was assessed, based on stream and shore organisms and an important ecosystem function for small freshwater streams. We used structural equation modeling to test our hypothesis and to quantify the effects of pesticide stress. Our study was conducted in the context of the trinational Upper Rhine Graduate Academy and may facilitate joint efforts of the European member states to decrease pesticide risk for non-target organisms and ecosystems not only in the Upper Rhine Region, but trough out the European Union.