Biodiversity in running waters is threatened by an increased severity and incidence of low-flow extremes resulting from global climate change and a growing human demand for freshwater resources. Although it is unknown how and to what extent riverine communities will change in the face of these threats, considerable insight will be gained from efforts aimed at quantifying habitat size-related controls on the trophic relationships among taxa in streams experiencing extreme flow loss. Here we report on a detailed space-for-time survey of replicate stream food webs sampled along the perennial- to-drying continuum in each of fourteen different intermittent South Island, New Zealand streams. We quantified several structural attributes of food webs at fifty-eight sites, including two taxonomically-based metrics (web size, predator:prey ratio) and three stable isotope-based metrics (food chain length [FCL], trophic area, d13C range); we also quantified habitat size-, disturbance-, and resource-related covariates at each site. Food web structure varied widely across sample sites within and across study streams and much of this variation was explained by habitat size. Consistent with our predictions, we found that food webs became smaller (ca 30 to ca 15 taxa, ca 20-fold reduction in stable isotope-based trophic area) and shorter (maximum trophic position [FCL] from 4.1 to 2.0, 25% reduction in predator:prey ratio) as we moved from the largest to smaller habitats. These results, and a comparison of our findings with those from a similar assessment conducted in perennial streams, suggest that there are perturbation thresholds which may trigger food web collapse when exceeded, and further imply that food webs may ultimately be 'sized' to minimum flows rather than average flow conditions. Our work provides a basis for making general predictions about how habitat contraction, and flow loss in particular, may affect communities and additionally provides insight on mechanisms warranting further attention.