Knowledge about the distribution and diversity of wetlands has become an essential tool for environmental management and policy-making. Yet, while recent estimates indicate that 27% of the area of Colombia is covered by wetlands and despite a number of regional studies, information about the diversity of wetlands nationally is scarce. In response, we present a national wetland classification system that is based on an ecological approach, from the perspective of wetland scientists, and which builds upon the assumptions underlying the flood pulse concept and hydrogeomorphic approach. Thus, the approach and structure of the Brazilian wetland classification system are used, with geomorphological adjustments made according to Colombia’s topography. The classification is hierarchical, multi-scale, functional, and organized according to four levels (system, macroregion, subsystem, and class), with the wetland diversity of Colombia represented nationally by 89 macrohabitats across marine-coastal, inland, and anthropogenic systems. The primary purpose of this classification is to provide integrated and organized information on the distribution and diversity of Colombian wetlands that will serve as a baseline for transparent environmental policy-making.