Trees species in the mangrove genus Avicennia can shed canopy parts when exposed to adverse environmental conditions, such as increases in porewater salinity. The individual-based model BETTINA enables the quantification of the tree’s water use depending on its allometric characteristics. It thus provides a tool to model the equilibrium between plant size and density in a mangrove stand and porewater salinity. When the model is coupled with a simple water balance approach, the water use of trees corresponds to water uptake from the soil and, in combination with water fluxes, an increase of salinity in the root zone. Annual variations of the sea level, the tidal regime, groundwater inflow, and precipitation have an impact on the equilibrium of the combined system. Higher salinities lead to lower potential gradients and reduced water uptake of the plant. With a combined modelling approach (single tree model BETTINA with a simple water balance approach), we examined the dampening effects of consecutive partial canopy loss for the survival of the tree. We found that (i) the tree is able to decrease water demand and uptake and thus may reduce the tree’s effect on soil water salinity, (ii) the reduced branch length leads to a reduced xylem flow resistance, and (iii) the reduction in height has a small positive effect on the water potential gradient between leaves and soil. Individual-based models can enhance our understanding of the regulating impact of the partial canopy loss on water balance in the combined plant-soil system.