In this study, we assess the costs and benefits of dynamic management of water storage to improve flood control in a system of wetlands. This management involves releasing water from wetlands ahead of (e.g., a few hours or days before) a rainfall event that is forecasted to produce flooding. Each project site may present different challenges and topographical conditions, however as long as there is a relatively small hydraulic gradient between the wetland water surface and the drainage ditch (e.g., >0.9 m), wetlands can be engineered for the purpose of flood control. We present a case study for a system comprised of four wetland areas encompassing 925 acres in the coastal plain south of Houston, Texas. The benefit–cost analysis shows that, in general, the benefits of wetland ecosystems far surpass the costs of construction and maintenance for all considered periods of analysis and assumed degrees of dynamic management of wetland storage. The analysis also shows that the benefit/cost ratios increase over the period of analysis. Considering flood protection only (e.g., not considering the value of other ecosystem services), as long as dynamic management of wetland storage increases flood protection by about 50% compared to that with no management (e.g., a typical wetland with no controlled release of water), the construction of a wetland system would have a benefit/cost ratio of at least 1.9.