When non-perennial stream reaches, dry-phase refuges retain some water, or at least remain damp, enabling aquatic organisms including macroinvertebrates to survive. However, human pressures including physical habitat modification alter refuge accessibility, diversity, extent and quality. Whereas homogeneous channels may have few accessible, high-quality refuges, damming can hold up water, potentially creating artificial refuges. It is thus unclear how anthropogenic habitat modification alters refuge quality and thus community recovery after water returns. We addressed this knowledge gap in the non-perennial, seasonally intermittent headwater reaches of three chalk streams in south England, one with higher, intermediate and lower levels of anthropogenic modification. We predicted a negative relationship between modification and macroinvertebrate community recovery. We conducted physical habitat surveys, measured water quality variables and sampled communities four times at two-month intervals starting in the month of lowest flows, at four sites on each river, from downstream perennial reaches to upstream intermittent reaches. We calculated metrics to summarize community characteristics then quantified differences between the ‘most recovered’ communities (i.e. those at sites which had dried then had most time to recover) and other communities. Supporting our prediction, recovery was greater on the least-impacted river and lower on the most-impacted river, and dissolved oxygen concentrations and sediment composition influenced recovery. In addition, the least-impacted river was the only one on which we recorded a nationally rare non-perennial-specialist mayfly. However, the most highly modified site retained ponded surface water upstream of a weir, potentially promoting upstream survival but also preventing colonization of upstream from downstream reaches. As river drying increases even in cool, wet countries such as England, maintaining and restoring natural habitats that include a range of dry-phase refuges is key to supporting the resilience of aquatic communities.