Transport of radionuclides from a repository to the biosphere is calculated in the presence of varying boundary conditions. This may occur in Sweden, for example, during post-glacial rebound. To calculate the transport of radionuclides, the flow field has to be calculated at each time step. An alternative approach is to determine the flow field at certain time intervals; i.e., modelling the dynamic flow system as a sequence of punctuated steady states. This can be done in a rather simple way by using the Channel Network model (CNM), in which radionuclide transport is calculated by particle tracking. Intuitively one would expect such a simple procedure to be permissible and lead to small errors if the time intervals are so short that only small changes in flow rates and flow directions take place. In this paper, the technique is applied to a study case. This describes a repository located at a sub sea level location outside the coastline; where, owing to the land lift that is taking place in Scandinavia the coastline is advancing towards the repository. An important issue to be determined is the minimum number of time intervals that need to be used in order to obtain a reliable solution to radionuclide transport. It is found that the number of time intervals needed is strongly dependent on the variation in the boundary conditions. For the changing conditions used in the example tested, a number on the order of 5–9 time intervals allows a sufficiently good representation of the transport.