While interest in the ecological effects of depleting groundwater resources is increasing, little is known about the effects of groundwater drawdown on biogeochemical processes in the hyporheic zone. This study aims to elucidate the coupling and feedback mechanisms between flow and biogeochemistry in the hyporheic zone of three streams with different flow regimes (from intermittent to perennially gaining and losing) in the Maules Creek Catchment (NSW). The variation in flow regime is used as a proxy for groundwater drawdown. Stream reaches were characterised based on surface flow duration, hyporheic zone flow thermal regimes, inorganic tracers and head gradients. The hyporheic zone for the stream reaches was sampled at two depths 0.4 and 0.8 m for the characterisation of dissolved organic matter and inorganic redox-sensitive species. The biogeochemical conditions in the regional groundwater were characterised using a network of observation bores. The results illustrate that hyporheic zones of gaining reaches generally had oxic regional groundwater discharging into them, while losing reaches generally had steep redox-gradients and anoxic conditions (low dissolved oxygen and high Fe2+) developing a few tens of centimetres into the streambed. The characterisation of organic matter revealed that while infiltrating surface water DOC may be important in driving redox-reactions, buried sedimentary organic matter plays an equally important role. Rapid degradation of organic matter leads to anoxic conditions favourable for anaerobic microorganisms. The findings have implications for the prediction of impacts to water quality in hyporheic zones and streams subject to groundwater drawdown caused by agricultural and mining activities.