Fractured rock masses below the water table are a problem in underground excavations because of their low strength and high permeability. Nowadays, these negative connotations can be reduced with techniques such as injection of cement, microcement, or resins grouts. These materials increase the rock mass cohesion while reducing the flow of water through the discontinuities. This paper describes the work carried out to design a waterproofing screen for a three-storey underground basement located in a building near the Bilbao estuary (Northern Spain) and with problems of water seepage from the river. First, a survey of the rock mass is carried out. This survey shows the presence of highly fractured zones and the variability of the permeability as functions of the fractures. Subsequently, the effect on permeability caused by the injection of cement grouts and microcement is studied by means of two pilot injection boreholes and eight control boreholes. Finally, a behavioural model is proposed to explain the heterogeneity observed in the radius of influence of the injection. As a result, a waterproofing screen with three types of treatment is designed: An ordinary treatment with cement grouts, an intensive treatment with microcement grouts, and an isolation treatment with cement-bentonite grouts.