The duration, intensity and frequency of hydrological droughts are predicted to increase significantly over the 21st century globally, threatening the long-term stability of lotic communities. In this paper we examine the recovery and recolonization of macroinvertebrate taxa in ephemeral and near perennial reaches of the River Lathkill (UK) after a supra-seasonal drought event. Following flow resumption, species accumulation (recolonization) occurred rapidly over a 4-month period, with a steady increase observed thereafter. Taxonomic richness was significantly higher in the section with near perennial flow after the first month of the study than the naturally ephemeral reach. Serial correlation was observed in the near perennial section but not in the upstream ephemeral reach. Serial correlation in the near perennial section may reflect: (1) the ongoing process of recovery or (2) the macroinvertebrate community following a new ecological trajectory. Our results suggest that supra-seasonal droughts may cause initial reductions in lotic diversity during stream desiccation events but may re-set ecological succession and/or temporarily provide new ecological niches, thereby supporting increased taxonomic diversity when the full range of hydrological conditions are considered. Quantifying the recovery of ecological communities following supra-seasonal drought can provide information to help develop ecologically effective conservation and management strategies.