Although it is widely acknowledged that a decline of freshwater biodiversity jeopardizes the functioning of freshwater ecosystems, the large number of (human-induced) pressures jointly acting on these systems hampers managing its biodiversity. To disentangle the magnitude and the temporal effects of these single and interacting pressures, experiments are required that study how these pressures affect the structuring of natural communities. We performed experiments with naturally assembled invertebrate communities in 36 experimental ditches to assess the single and joint effects of environmentally relevant concentrations of two commonly co-occurring stressors: fertilizer inputs and neonicotinoid insecticides, in this case thiacloprid. Specifically, we explored whether these agrochemicals result in sustained changes in community structure by inspecting divergence, convergence and short- /long-lived dissimilarity of communities, when compared to a control treatment. Our results indicate strong impacts on the abundance of different taxa by exposure to the agrochemicals. However, we found no effect of any treatment on total abundance, taxon richness or convergence/divergence (measured as beta dispersion) of the communities. Moreover, we found contrasting responses when both joint stressors were present: when considering abundance of different taxa, we observed that fertilizer additions reduced some of the thiacloprid toxicity. But when assessing the community structure, we found that exposure to both stressors consistently resulted in a more dissimilar community compared to the control. This dissimilarity was persistent up to four months after applying the agrochemicals, even though there was a turnover in taxa explaining this dissimilarity. This turnover indicates that the persistent dissimilarity can potentially be attributed to a rippling effect in the community rather than continued toxicity. Such shifts in natural freshwater invertebrate communities, months after the actual exposure, suggests that stressors may have important long-term repercussions for which may subsequently lead to changes in ecosystem functioning.