Environmental risks in gypsum karst areas such as geomechanical problems as a result of gypsum dissolution or the vulnerability of the aquifers due to the unretarded transport of pollutants are mainly determined by the karst conduit system. Therefore, in order to provide a reliable basis for risk assessment, an adequate hydrogeological characterisation of the conduit system is required. A newly developed modelling tool is presented, which has been designed to support the characterisation of the conduit system of gypsum karst aquifers by simulating short-term fluctuations of solute concentrations and temperatures of the spring water. Both solute concentration and temperature of the spring water depend on the geometric and hydraulic properties of the conduit system. If only one of these parameters is analysed a unique identification of the structure of the conduit system may not always be obtained. Unsteadystate simulations of both heat and solute transport, however, show that different conduit systems, which are equivalent with respect to spring signals of one parameter, can be distinguished by taking into account a second parameter.