Intermittent rivers are temporally dynamic, shifting between lotic, lentic (ponding) and dry habitat phases, yet almost all research effort has focussed on the lotic phase, with limited research attention on the lentic and dry phases. Information regarding the biological diversity of the lentic phase is vital to quantify the total aquatic biodiversity, their use as flow refugia, and the long-term conservation and management of intermittent rivers. In this study, we compared the diversity and composition of macroinvertebrates from perennial, intermittent and ponded sites in two intermittent rivers in the United Kingdom. We examined whether instream ponding provided refugia for lotic taxa and a habitat for newly colonising taxa. A total of 129 taxa (perennial - 86, intermittent - 82, ponding - 78) were recorded. Instream ponds were found to support heterogeneous communities compared to flowing sites. Twenty-two percent of taxa were recorded only from ponded sites, many of which were lentic specialists, while 38% of taxa persisted in instream ponds after flow had ceased. Results from this study highlight that instream ponds provide an important flow refuge for macroinvertebrates including rheophilic taxa, which move into instream ponds when channels become longitudinally disconnected, and makes a significant contribution to aquatic diversity in intermittent rivers, providing suitable habitat for newly colonising taxa. Aquatic diversity in intermittent rivers may have been underestimated historically, failing to acknowledge the ecological contribution of the lentic phase. Incorporating the ponding phase alongside the lotic phase will ensure the total aquatic biodiversity of intermittent rivers is quantified and effective biodiversity conservation and management strategies are employed.