This paper identifies and assesses the economic value of the main natural benefits relating to the complex system of wetlands (CSW) belonging to the San Juan River in the Colombian Magdalena Medio. This is a region rich in biodiversity and natural resources, which in the past was hit by violence and the actions of different armed groups. Benefit estimation takes into account diverse monetary valuation techniques, such as market prices for direct wetland uses and the transfer of benefits, for the assessment of indirect use and non-use values. The results reveal that the most important values relate to ecotourism (60.1%) as a possible future use of the CSW, the benefit of preventing flooding (28.4%), and the biodiversity that inhabits the area (6.7%). All three values represent the total economic value of the CSW. This research also finds that the benefits of the ecosystems currently provided by the CSW exceed the opportunity cost, represented by the total conversion of the area to livestock. Lastly, the net present value (NPV) of 25 and 75 years, relating to the benefits of the CSW, exceeds the income from the conversion of land to livestock, revealing profitable investments in conservation and ecotourism projects.