Contrary to previous hydrogeological assumptions, we now know that drift deposits and fracture systems in crystalline rocks can constitute important aquifers in the Scottish Highlands and other montane environments. Groundwater from these aquifers usually has an important influence on the hydrology, hydrochemistry and ecology of upland river systems. Tracer-based research in the Girnock burn catchment in the Cairngorms revealed that groundwater comprises at least 30% of annual runoff. Groundwater often enters stream channels via drift deposits in valley bottom areas, which appear to be fed from recharge areas on the catchment interfluves. A range of groundwater sources exist in the catchment reflecting the complex solid and drift geology. These account for spatial differences in stream hydrochemistry and the spatial delineation of groundwater discharges to rivers and riparian zones. Areas where groundwaters enter the stream channel directly can have profound ecological implications. Most obvious are low rates of salmonid egg survival where chemically reduced groundwater discharges through the hyporheic zone. However, it is argued that only further research will reveal the full significance of groundwater–surface water interactions to the ecological status of Scottish rivers.