Flood effects on benthic algal communities grown upon three common substratum types were assessed in a gravel-bed stream. Microform bed clusters (MBCs) and, to a lesser extent, boulders conferred resistance on their associated periphyton communities (i.e., reduced flood-induced biomass loss; functioned as refugia) relative to cobble/gravel substrata. On all substrata, flooding significantly reduced the relative abundance of Diatoma hiemale, and increased the relative abundance of Gomphonema minutum f. syriacum and/or Ampithrix sp. Long-term (>4 months) sampling indicated that MBCs generally supported more algal biomass than did boulders, which, in turn, supported greater biomass than cobbles/gravels. Manipulation of the abundance of refugial structures (e.g., MBCs) could possibly alter productivity of flood-prone gravel-bed streams. Stream periphyton biomass models may be improved by explicit consideration of the effects of refugial substrata. The interstitial spaces of MBCs may constitute a unique habitat, and deserve futher study.