Flow intermittency can be difficult to measure at a high spatial and temporal resolution. In particular, headwater streams can cease and resume flow at very fine temporal and spatial scales. Small, robust electrical resistance (ER) loggers offer a low-cost solution to measure saturated flow conditions from which streamflow timing can be accurately inferred. Here, we used ER loggers modified from HOBO light and temperature sensors to measure flow intermittency across an Alpine stream network in Val Roseg, Switzerland. Our goals were to: i) accurately measure the presence/absence of surface water, ii) validate measured values with field surveys, iii) develop metrics to characterize flow/temperature regimes and ordinate sites along an intermittency gradient, and iv) relate measures of flow intermittency to benthic community structure and function. Results indicate the method was robust to assess flow intermittency, and showed that intermittency affects benthic communities particularly through changes in the trophic base of food webs. We thus show that ER sensors are a viable option for characterizing flow intermittency and its ecological effects at fine scales, and discuss the utility of using ER sensors in other climatic and geomorphological settings.