The separation of base flow from discharge records is an important issue in hydrology. The objective of this paper is to develop a base flow separation algorithm, based on groundwater theory, in which the shape of the aquifer is taken into account and for which the parameters can be estimated from river discharge measurements. For this purpose, an analytical solution to the linearized Boussinesq equation for realistic aquifer shapes and temporally variable recharge rates is derived. This solution is combined with a mass balance at the land surface in order to construct the base flow separation algorithm. The parameters of the base flow filter are calculated on the basis of the same analytical solution. Comparison of the results of the new algorithm to existing base flow separation methods shows the need for a physical basis for base flow filters.