Nature-based water management is rising as an alternative approach to engineered water management. Nature-based water management makes use of ecological, hydrological, and morphological processes of natural rivers in designing river management policies. Furthermore, it helps conserving or restoring these natural processes for environmental purposes. Next to changes in water management, changes in the earth’s climate are occurring, which decrease the water flow in summer and autumn and increase the flow in winter. These changes will affect river uses and might cause conflicts between them. The river uses studied in this research are environment, navigation, and flood protection and an integrated model is developed to answer the research question: What conflicts arise between environment, navigation, and flood protection when nature-based water management policies are implemented under different water flow scenarios and how can insights in these conflicts be used in the policy-making process? The system dynamics (SD) modelling method has been used, because SD enables integration of physical, social and economic factors influencing water resources while addressing inter-sectoral, long-term problems. The scope of the model has been set to analysing a side channel as a nature-based water management example. The model has been built up of four sub-systems that are interrelated: the river system (including a main channel, side channel, and floodplain), the environmental system, the navigation system, and the flood protection system. The model results show that no conflicts arise during high water inflows. Furthermore, environment and flood protection or navigation and flood protection can find a solution that is beneficial (0r neutral) for both during low water inflows. However, the environment requires a side channel that is connected on both its ends – and therefore has a year-round water flow –, while navigation prefers a side channel that is only connected on its downstream end in order to prevent lowering of the water level in the main channel during low water inflows. Insights for policy-makers are found in five ways. First, the conflicts between river uses do not necessarily arise regarding the side channel per se – but concern the configuration of the side channel. Secondly, the conflicts strongly depend on the changes in water inflow due to climate change. Third, attention should be paid to compromises that are made. The side channel connected on one side can be seen as a compromise between nature and navigation and it indeed eliminates the negative effects on navigation, but it strongly reduces the benefits for nature. Fourth, for nature-based water management to be truly effective for environmental purposes, integration of several measures is required. Finally, the model showed that system behaviour is strongly dependent on fixed standards (e.g. maximum amounts of vegetation and presence of summer dikes). The model that was developed in this research can also be used to study the effects of river channel widening, floodplain widening, summer dike removal, and changes in floodplain vegetation management.