This paper presents a method for establishing segment scale typology for the Andean rivers of Colombia. The method incorporates physical and ecological aspects and combines inferences of structural stability and metabolic activity. The classification of river segments is based on the assignment of two non-dimensional descriptors. The first descriptor involves aspects related to structural stability of the channel, whereas the second descriptor includes factors that affect the metabolic activity of planktonic communities in the water column and biotic communities on the bed. Each descriptor can adopt values that are divided into two categories, high and low. Both descriptors are organized orthogonally. A bidimensional 2 × 2 matrix is created, where the x-axis represents the current structural stability of the channel and the y-axis represents the metabolic activity. A case study that combines a set of thematic layers using GIS is presented for the Cundinamarca region in Colombia. Most of the river segments (97%) in Cundinamarca correspond to type 2 or 4. We provide data from macroinvertebrate samples to compare the obtained types with the actual biological communities present in the region. This method, which can be useful for scientists, managers and water planners, compares similarities and differences between water body systems, compiles basic information in a brief and clear manner and locates monitoring and reference sites for bioassessment studies.