Balancing coastal urban development with species conservation and habitat protection can be challenging for managers especially where good quality ecological data is lacking. Primary freshwater crabs (Austrothelphusa species) of the family Gecarcinucidae (formerly Parathelphusidae) that occupy inland creek systems are also present in small coastal areas. In coastal regions, habitat loss in response to urbanisation and transformation of natural water channels to concrete drainage lines is a major threat to coastal crab populations. We provide data showing that one species, A. transversa, still exists in natural creek lines in Townsville, but not in engineered creek channels a little further downstream in some cases. Continued urbanisation means that populations will be under threat as the city continues to expand, transforming further natural creek lines to engineered concrete channels. Whether the absence of crabs in urban channels is due to increased predation from fish present in the permanent water (including noxious Oreochromis mossambicus), water chemistry differences, increased competition for food and shelter, or simply because this species cannot burrow in concrete channels to complete important lifecycle stages, warrants further investigation. Evidence is also provided that A. transversa coexists in natural waters with another freshwater crab species, the varunid, (Varuna litterata). The importance of management strategies for both species is discussed, particularly under continuing habitat squeeze with expanding coastal development.