This article describes the long-term effects on the macro invertebrate and zooplankton community in outdoor experimental ditches after a single application of the insecticide chlorpyrifos. Nominal concentrations of 0.1, 0.9, 6, and 44 μg/L of chlorpyrifos were applied to two mesocosms each, while four served as controls. Both macroinvertebrates and zooplankton were sampled from 4 weeks before to 55 weeks after treatment. The macroinvertebrate and zooplankton data sets were combined into one data set and analyzed using the multivariate ordination technique “redundancy analysis.” The method provided a clear description of the effects on the invertebrate community in time while still showing the effects at the species level. Crustacea and Insecta showed a rapid, concentration-dependent decrease in numbers after insecticide application (direct effects). An increase in gastropods and Oligochaeta was found, suggesting indirect effects. The start of recovery of the invertebrate populations affected was found to depend not only on the susceptibility of the taxa but also on ecological characteristics, such as the length of the life cycle. A no-observed-effect concentration of 0.1 μg/L could be derived both at the species and the community level. Safe concentrations, based on no-observed-short-term-effect levels for some characteristic indigenous taxa susceptible to chlorpyrifos, also appeared to protect the total invertebrate community in the long term. The invertebrate community at all treatment levels was considered to have recovered after 24 weeks posttreatment.