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Intermittent and ephemeral streams in dryland regions often fragment into isolated pools as they dry. In general, pool fragmentation provides favorable conditions for aquatic algae and plant growth and should therefore result in foodweb reliance on aquatic algal resources over comparatively-recalcitrant terrestrial plant litter. However, differences in pool hydrology and morphology might substantially alter organic matter dynamics and, thus, alter the trophic base of aquatic consumers. We tested whether 1) taxa composition or 2) pool hydrology and morphology might affect the trophic base of macroinvertebrate assemblages in dryland stream pools. We used stable isotope analysis to assess the hydrological regime (d18O and d2H) and trophic structure (d13C and d15N) of fragmented pools within an ephemeral dryland stream. We compared differences in pool morphology, evaporation rates, and groundwater connectivity to dietary-mixing model results for macroinvertebrate assemblages over 2 seasons. Differences in macroinvertebrate assemblage composition were not consistently related to pool hydrology, morphology, or season. We found that filamentous algae and aquatic biofilms supported macroinvertebrate assemblages to a greater extent than did terrestrial plant litter. Biofilm assimilation was higher in highly-evaporated pools, and terrestrial plant litter assimilation decreased as pools became smaller and aquatic vegetation cover decreased. Overall trophic diversity decreased with increasing aquatic vegetation cover. This study suggests that hydrological and morphological gradients across pools drive differences in the trophic base of macroinvertebrate assemblages, potentially through variation in organic matter productivity and biomass. Consequently, natural variability in groundwater connectivity and pool morphology likely enhances trophic diversity across this ephemeral riverscape.