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We developed an uneven-aged forest economic decision-making framework that combines: (i) a size-structured matrix model, based on growth and mortality predictions of a dynamic process-based forest landscape model, (ii) an optimal control model that determines the dynamics of control and state variables, which in turn are defined by tree harvesting and forest stock, respectively, and (iii) a water yield function that depends on changes in the leaf area index (LAI), the latter being affected by forest management. This framework was used to simulate the effects of economic-driven harvesting decisions on water yields on a catchment of South-Western Swiss Alps when both timber and water benefits are considered. Water benefits are estimated as environmental prices considering current water demands for drinking, irrigation and hydropower production. We simulated optimal harvesting decisions given the initial forest structure at each 200 m × 200 m grid cells, a set of restrictions to harvesting, and specific species survival, recruitment and growth probabilities, all of which are affected by the stand’s LAI. We applied this model using different harvesting restriction levels over a period of 20 to 40-years, and accounting for single and joint timber and water benefits. The results suggested that at the environmental prices estimated at the catchment area, water benefits have a slight influence on harvesting decisions, but when water is accounted for, harvesting decisions would include more tree species and different diameter classes, which, in principle, is expected to favor more diverse forest structures.