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Abstract Controlled drainage with subirrigation (CDSI) using surface water contributes to freshwater availability by recharging, retaining and discharging water. However, CDSI systems affect regional hydrological fluxes, which requires adequate regional planning and management. This study aims to (i) investigate to what extent regional upscaling of CDSI can be supported in relation to surface water availability, using a system dynamics model (SDM) and (ii) identify how an SDM can support decision making of water management authorities. An SDM was developed to simulate changes in hydrological fluxes and water levels resulting from CDSI upscaling from the local to the regional scale. An SDM was used as it is able to capture key non-linear feedbacks within the water system, such as those between (i) surface water and groundwater, (ii) groundwater and unsaturated zone, (iii) regional water supply and weir management. The model provides insight into changes in hydrological fluxes due to CDSI upscaling, without long computational times and the complexities of spatially distributed models. Simulations show non-linear propagation of hydrological fluxes, where three phases can be identified for different degrees of upscaling: (i) sufficient surface water availability, (ii) surface water availability decreases due to subirrigation, and (iii) insufficient water availability due to overexploitation. These phases are related to regional and local water management strategies controlled by water management authorities and farmers, and to geohydrological characteristics. In conclusion, the SDM can support early-stage strategic planning on the feasibility of CDSI upscaling and facilitate discussions between stakeholders by efficiently visualizing and quantifying associated hydrological effects.