The impacts of current and alternative wheat crop protection programs were compared in outdoor pond mesocosms in a 10-month long study. Realistic exposure scenarios were built based upon the results of modelling of drift, drainage and runoff of pesticides successively applied under two environmental situations characteristics of drained soils of northern France. Each situation was associated to two crop protection programs ("Conventional" and "Low-input") differing in the nature of pesticides used, number of treatments and application rate. Both programs induced significant direct negative effects on various invertebrate groups. Bifenthrin and cyprodynil were identified as the main responsible for these effects in conventional and low-input program, respectively. Indirect effects were also demonstrated especially following treatments with cyprodynil. Litter breakdown was significantly reduced in all treated mesocosms as the functional consequence of the decrease in the abundance of shredders (asellids, Gammarus pulex) illustrating the link between structural and functional effects of pesticides on macroinvertebrate communities. Recovery was observed for many taxa before the end of the study but not for the most sensitive non mobile taxa such as G. pulex. No influence of the agropedoclimatic situation on the effects was shown, suggesting than the main impacts were associated to inputs from drift. The results confirm that the proposed low-input program was less hazardous than the conventional program but the observed structural and functional impact of the low-input program suggest that further improvement of alternative crop protection programs is still needed.