The effects of agricultural drainage on fish and benthic invertebrate communities are of increasing interest as attempts are made to mitigate anthropogenic effects on natural populations. A recent study concluded agricultural drains in southwestern Ontario are functioning as fish habitat and that there are no differences between the assemblages in drains and reference water courses of comparable size. Agricultural drains are subject to periodic maintenance actions, including full bottom cleanouts and bank disturbance, and previous work suggests that populations are recovering post maintenance. We present preliminary results on monitoring the recovery of fish and benthic invertebrate assemblages for 6 months following maintenance in four agricultural drains in southwestern Ontario. Drains were paired with reference watercourses of similar size, and a BACI design was employed to quantify recovery of assemblages. Drains and their references were sampled intensively to one month following maintenance, then at 6 months following maintenance, and will be sampled again at one year. During this time fish and benthic invertebrate assemblages, as well as habitat, were sampled. A greater understanding of recovery time will allow better management of drain maintenance practices.