The objectives of this study were to understand how reductions in groundwater level and baseflow affect the ecology of stygofauna in the hyporheic zone, and thence, to develop conceptual models to aid understanding of hydroecological responses to groundwater drawdown. We examined effects of reduced baseflow permanence by sampling gaining and losing reaches of streams with varying intermittency and perenniality, in wet and dry periods. Stygofauna and hydrochemistry in upwelling and down-welling hyporheic zones were sampled from mini-piezometers <1m deep, and in the aquifer, from groundwater bores. The study was conducted in the upper Bremer River catchment in southeast Queensland and the Maules Creek catchment in northern NSW. In the Maules catchment, a rich stygofauna inhabited creek systems with deep alluvium and strong hydrologic connectivity to the regional aquifer. The Bremer catchment also had a rich stygofauna, but was contrasted by creeks with very thin alluvium (< 0.5m) overlying relatively impermeable strata, albeit still fed, to varying degrees, by groundwater discharge. In both catchments, streams with intermittent flow regimes supported a rich stygofauna demonstrating that ecosystem processes and function are maintained even during periods without surface flow. As hypothesised, losing/down-welling stream conditions supported few stygofauna. In contrast, gaining/upwelling conditions supported a rich stygofauna. The narrow vertical extent of the hyporheic zone means that only small changes in groundwater levels may switch the direction of hydrologic exchange from gaining/upwelling to losing/down-welling and thus change the ecological conditions for stygofauna and stream ecosystem function. This is relevant where groundwater drawdown from activities such as mine dewatering, coal seam gas extraction and irrigation for agriculture, potentially threaten stream ecosystem processes and function.