Seeper is a one-dimensional finite-difference model for simulation of water flow, solute transport and reactions of inorganic pollutants (As, Cd, Co, Cr, Cu, Mo, Ni, Pb, Zn) in unsaturated soils. The main focus in the development of Seeper was a simple and concise formulation for ease of use while at the same time providing sufficient accuracy for seepage water prognosis. The transport module is capable of modelling transient conditions. The mobility of trace elements is modelled via transfer functions to reduce the required input data and simplify the application of the model. This article introduces Seeper and describes the integrated algorithms and its utilization within the framework of percolation water prognosis. The current version of Seeper and its manual are available online at http://www.geochemie.uni-bremen.de/downloads/seeper.