Reptiles are rarely included in urban freshwater biodiversity monitoring and conservation. We explored the global persistence of freshwater dependent turtles, lizards, crocodilians and snakes in cities with a population greater than 100,000 using species occurrence data in online databases from a five-year period (2013–2018). We then used ecological niche models to help identify the locations of suitable habitats for three freshwater reptile species in Sydney, Australia. Our Global analysis showed that sightings of a majority of known species of crocodilians and freshwater turtles were recorded in databases within this 5-year period in contrast to about one in three freshwater lizard species and one in ten freshwater snake species and that freshwater reptiles were observed within 50 km of the center of 40% of the 3525 cities. While global databases hold substantial recent species occurrence records for some regions, they contain very little data for large parts of the world. Modelling showed that potential suitable habitat for the three freshwater species in Sydney was distributed across areas with different levels of urban development. The persistence of populations of freshwater reptiles in and around a large proportion of the world’s cities show that this group can play an important role in urban biodiversity conservation.