Many rivers are classified as groundwater-dependent ecosystems (GDEs), owing to the contribution of groundwater to their base flow. However, there has been little explicit recognition of the way groundwater influences riverine biota or processes, how degrees of ecological dependency may vary, and the management implications ofthis dependency. The permeable beds and banks of these GDEs where surface water and groundwater exchange are termed 'hyporheic zones'. They are often inhabited by invertebrates, with varying reliance on groundwater, although the ecological roles of these invertebrates are little known. Upwelling hyporheic water can promote surface primaryproductivity, influence sediment microbial activity, and affect organic matter decomposition. In many intermittent streams, variable groundwater inputs alter the duration of flow or water permanence, and the duration and timing of these largely govern the biota and rates of many ecosystem processes (e.g. leaf decomposition). Not only is the physical presence of water important, thermal and chemical conditions arising from groundwater inputs also have direct and indirect effects on riverine biota and rates or types of in-stream processes. Differing degrees of dependency of rivers on groundwater mediate all these influences, and may change over time and in response to human activities.Alteration of groundwater inputs through extraction from riparianwells or changes in localwater table have an impact on these GDEs, and some current management plans aim to restrict groundwater extraction from near permeable river channels. However, these are often ‘blanket’ restrictions and the mechanisms of GDE dependency or timing of groundwater requirements are poorly understood, hampering refinement of this management approach. More effective management of these GDEs into the future can result only from a better understanding of the mechanisms of the dependency, how these vary among river types and what in-stream changes might be predicted from alteration of groundwater inputs.