In 1999, the Swiss Federal Railway began to construct the AlpTransit railway tunnel transecting the entire Swiss Alps (57 km). The tunnel will cross the Triassic Piora Zone, a highly weathered and fractured aquifer under high hydraulic pressure situated between crystalline rocks of the Gotthard massif and the southern Pennine nappes. We report the results of two fluorescent dye tracing tests to investigate the groundwater hydraulics associated with two losing west-flowing streams in the Piora Zone. The first dye test found the direction of groundwater flow in the aquifer to be opposite to the direction of the surface-water flow above. In contrast, dyes were detected in springs discharging in the Santa Maria Valley, located 6.5 km east of the surface water topographic water divide. A second, more thorough, dye tracing test confirmed our initial results and showed that water in the weathered Triassic Piora Aquifer moves hundreds of meters per day. The base of the aquifer is ~250 meters above the proposed AlpTransit tunnel which will be drilled through unweathered and unfractured dolomite/anhydrite-sequences. Our dye tracing tests, combined with the exploratory tunnel Polmengo, predict that the AlpTransit railway tunnel will be unaffected by the overlying aquifer and its complex hydraulic system.