Ecosystem services are a telling concept to discuss the integrated management of natural resources, such as integrated water and soil, with non-academic stakeholders. Stakeholders have different perceptions regarding the management of various ecosystem services, which is challenging when aiming to develop and foster sustainable ecosystem management. We performed a stakeholder analysis as part of a social-ecological study in preparation of a decision support system for integrated water management within the Lake Manyara sub-basin (LMSB), Tanzania. The area includes a National Park and UNESCO Biosphere Reserve. A group discussion listed 26 stakeholders, categorized according to the sector, influence, and interest. The stakeholders were grouped into six functional categories: local Non-Governmental Organisations (NGOs), other civil society groups, Belgian and international NGOs, authorities, academics associated to international donors and the private sector. We empirically identified advantages, shortcomings and associated risks when performing a stakeholder analysis with an interest–influence matrix. Confounding factors may include, e.g., the omission of important stakeholders, a different understanding of ‘influence’ and ‘interest’, or the omission of fragile groups. Instead of ‘low’ or ‘high’ interest and influence, we propose the terms ‘supportive’, ‘potentially supportive’, ‘unsupportive’, ‘not interested’, ‘low or no influence’ and ‘antagonistic’. Further, we consider stakeholders who directly extract resources from the social-ecological system (SES) as a separate category, because of their direct dependence and impact on the SES. This improved stakeholder analysis framework for developing decision support systems in water basins can contribute to better analysis, understanding and management of aquatic social-ecological systems in general.