This paper describes an 11-year experience of scientific cooperation between different partners for sustainable development and sound technologies, in the field of sanitation and wastewater treatment. The Faculty of Engineering (University of Trento, Italy), the Faculty of Science (University of Mahajanga, Madagascar) and other local NGOs and administrations cooperate to foster research, mainly for anaerobic treatment and practical, effective solutions. This work describes strategies, efforts and practical solutions developed to carry on a scientific research and practical solutions in Mahajanga as a result of a multi-sectorial cooperation. The aim of this kind of collaboration was also to foster local, independent research and to support the new specialization course in waste and wastewater treatment at the local Faculty.