Flow intermittency can have a destabilising effect on stream food-webs by reducing algal abundance, changing the breakdown rates of particulate organic matter, and through the elimination of top predators. Contributions to surface runoff from groundwater can play an important role in maintaining baseflows in intermittent streams, thus providing a potentially stabilising influence on food-webs. Using stable isotopes (δ13C and δ15N), we investigated the role that baseflow has in shaping the food web structure in surface and hyporheic habitats of intermittent streams in two catchments in eastern Australia. Preliminary results indicate that non-filamentous algae and/or diatoms colonising benthic cobbles and rocks, and not particulate organic matter, are the primary basal food resource for higher trophic levels (macroinvertebrates and fish) in both stream systems. Furthermore, isotopic signatures of both basal resources and higher order consumers indicate groundwater contributions play an important role in sustaining basal production in these systems. The implications of current and potential future groundwater drawdown due to human activities in these systems is highlighted.