Severe problems caused bu sudden uncontrolled flooding encountered during the construction of the Seikan Tunnel, Japan that connects the islands of Honshu and Hokkaido, could be anticipated and avoided by use of data on chemical compositions of seepage waters from boreholes and working surfaces, to recognize waters of short residence times. Four floodings occurred between February, 1969 and May 1976 before the significance of water compositional data was recognized; no flooding took place during the rest of tunnel construction. The 23.3 km long undersea part of the Main, Pilot and Service tunnels passes 100–200 m below the sea bottom under the Tsugaru Strait in Miocene volcanogenic marine sedimentary rocks, the so-called Green Tuff, which is a thick sequence of tuff, siltstones and sandstones altered by diagenetic and hydrothermal processes, regional and contact metamorphism, and broken by active faulting. Prior to construction, the rocks underlying the land and the Tsugaru Strait were studied by the Japan Railroad Construction Company using geologic, geophysical and oceanographic techniques, which yielded excellent understanding of the distribution of rock types and location of faults. Near-coastal rocks under the Tsugaru Strait contain waters of two types, seawater and meteoric water. Seawater is presently mixing with meteoric water that is remnant from emergent periods of the Pleistocene. Meteoric water also is being input from land. Seawater-meteoric water mixtures have interacted with Green Tuff rock at temperatures of 10–30°C and 1–40 bars to produce mostly clays and carbonate minerals, and to dissolve CaSO 4 minerals. Well interacted mixtures contain little K and Mg, and high levels of Ca and SO 4. An empirical factor, K × Cl, proved useful in deducing relative residence times of the fluids; K reacts rapidly and a rise in it is a secure indication of recency of input; Cl does not react significantly, making it of use for calculating mixing ratios, and it rises also with recency of input of fresh seawater. Plots of K × Cl vs distance along the service tunnel showed maxima above 5000 near places where seawater subsequently broke through. Similar plots along the pilot tunnel 100 m below, the construction of which was kept well in advance of the service tunnel, also showed maxima of predictive value when combined with structural information. Advance warnings permitted immediate actions to be taken to prevent disastrous flooding. Use of geochemical data, therefore, created a practical method of predicting events in complex geologic and geochemical situations. The predictions were of great importance economically, and critically needed to lower threats to lives of workers in the tunnel.