We report on an avian influenza virus (AIV) project implemented in the Manyame catchment between 2007 and 2011. This project was undertaken as collaboration between two larger programmes, GRIPAVI (Cirad) and SA-GAINS (PFIAO, Univ. of Cape Town). We found persistence of low pathogenic AIV in waterfowl between May 2007 and November 2008 and potential for AIV transmission between wild and domestic birds. The approach that we developed in this project, which integrated ecology and epidemiology (both academic and applied), has tremendous potential for future work in the domain of disease ecology at the wildlife/domestic animal interface.