The freshwater prawns of genus Macrobrachium with abbreviated larval development have been reported from a diversity of freshwater habitats (caves, springs and primary streams from so-long basins). Here we analysed 360 sites around the Mesoamerican region (Mexico, Guatemala and Belize). At each site, we measured temperature, salinity oxygen dissolved, pH, altitude and water flow velocity values. We documented the riparian vegetation and occurrence and abundance of Macrobrachium populations. All these values were analysed by multi-dimensional scaling and principal components analysis in order to identify key features of the environmental data that determine the habitat types and habitat diversity. The results show that there are Macrobrachium populations in 70 sites inhabiting two main habitats: Lotic and Lentic; and each one have fours subhabitat types. All are defined by altitude range and water velocity that involve the temperature and oxygen variables. In some specific areas, the karstic values on salinity and pH defined some groups. Within the lentic habitats, we identified the following subhabitats: (1) temperate streams, (2) neutral streams, (3) high dissolved oxygen, (4) multifactorial; and for lotic habitats, we identified: (5) water high carbonate, (6) moderate dissolved oxygen, (7) low dissolved oxygen, and (8) high altitude streams. All these subhabitats are located on the drainage basin to the Atlantic Sea, including places from 50 to 850 meters above sea levels and have specifically ranges from temperature, water velocity, pH and salinity for some cases. Also, the geological analysis from the basins where the Macrobrachium inhabit is located showed that the geological faults align with these habitat subdivisions. In this chapter, we discuss the environmental heterogeneity, morphological plasticity and their relationship to physiographic regions across the species ranges.