The method recently developed to include van der Waals interactions in DFT (Density Functional Theory) using Wannier functions is applied to small water clusters, characterized by hydrogen-bonding interactions. In particular, water hexamer represents a critical test case since it is relevant for the condensed phases of water and has four low-energy isomers with similar binding energies. We are able to achieve results close to those obtained by high-level quantum chemistry methods and we find that inclusion of van der Waals effects is crucial for an appropriate description of the hydrogen bonds and to get accurate dissociation energy estimates. The relevance of these results for DFT simulations of liquid water is finally discussed. (C) 2009 Elsevier B. V. All rights reserved.