The primary source of C and N for macroinvertebrate food webs can be highly variable within intermittent streams. We hypothesised that differences within and among streams are related to increasing competition for autochthonous resources as surface water dries while macroinvertebrate density increases. We measured δ13C and δ15N values of macroinvertebrates and their possible food sources from pools of varying hydrology along an intermittent dryland stream in the Pilbara, northwest Australia. We compared differences in community composition and food web structure between two time periods (the late dry season and then later, after floods resulting from cyclonic rainfall, in the early-mid dry season) of a range of pools varying in connectivity to shallow alluvial groundwater (AW). While community composition was largely unchanged, differences in overall macroinvertebrate abundance between sampling periods were highly related to the degree to which pools had become disconnected from AW in the dry season and subsequently evaporated. While δ13C and δ15N values for primary producers did not differ across pools or sampling periods, several macroinvertebrate orders (Ephemeroptera, Hemiptera and Diptera) had lower (more depleted) δ13C and δ15N values in the early-mid dry season. Layman metrics of food webs structure indicated that food webs were larger and more diverse in the early-mid dry season. However, Bayesian mixing models of C and N source contributions to macroinvertebrate production showed no preferred food source at any time, for any order. In addition, low δ13C values (≤40 ‰) for Ephemeroptera indicated that an unmeasured carbon source, perhaps derived from methane-oxidising bacteria, was contributing to macroinvertebrate food webs at times. We suggest that macroinvertebrates within intermittent streams consistently exhibit generalist feeding strategies due to the influence of high, long-term hydrological variation on community composition and available species pools.