Water research projects are often interdisciplinary and participatory in nature. Scientists and managers involved strive to create learning that advances science in various fields while providing benefits for society. They also face challenges of monitoring and evaluation (M&E) for accountability and measurement of impacts, required by funding agencies. In this paper we tested selected M&E processes and methods for their potential to increase capacity in a cross-cultural inter-disciplinary research setting of an urban water research project. A total of eight different qualitative and quantitative evaluation methods were assessed using two processes: self-evaluation by researchers, testing five methods; and the external evaluations by stakeholders, testing three methods. Both processes were found useful. Of the five self-evaluation methods tested, the Logical Frameworks method was deemed a good planning tool but not one contributing to learning. The qualitative (Factors of Success and Obstacles/Enablers) and the Best Case/Worst Case Scenarios quantitative method were effective learning methods. Tracking Change was found suitable for measuring learning. We recommended that a combination of methods be used in order to capture the full dynamic of projects in various stages. Explicit timelines for indicators and measures of project success are recommended for managing expectations of both researchers and funding agencies.