SUMMARYFinite element discretizations of flow problems involving multiaquifer systems deliver large, sparse, unstructured matrices, whose partial eigenanalysis is important for both solving the flow problem and analysing its main characteristics.We studied and implemented an effective preconditioning of the Jacobi-Davidson algorithm by FSAI-type preconditioners.We developed efficient parallelization strategies in order to solve very large problems, which could not fit into the storage available to a single processor.We report our results about the solution of multiaquifer flow problems on an SP4 machine and a Linux Cluster. We analyse the sequential and parallel efficiency of our algorithm, also compared with standard packages. Questions regarding the parallel solution of finite element eigenproblems are addressed and discussed.