Urbanization affects ecological communities but urban ecology has mostly focused on large and charismatic species. Water-filled tree holes and other ephemeral small standing waters in cities constitute unique but inconspicuous breeding habitats for a range of insects. Their biodiversity is not well known and how their communities respond to increased urbanization in particular, has rarely been studied. Using a Citizen Science Project, we investigated how urbanization (measured as imperviousness, human population density and altered temperature), additional environmental parameters (pH, electric conductivity) and detritus serving as a food source affected larval insect communities in artificial aquatic microhabitats. We found that these habitats were colonized quickly by a range of insect taxa. Their community abundance, richness and decomposition rates were largely stable across different levels of urbanization. Fine detritus content increased larval abundance. Community composition shifted strongly with urbanization. The most abundant and frequent species in our study, the exotic mosquito species Aedes japonicus, responded negatively to imperviousness. Aquatic microhabitats could be shown to be important habitats for aquatic insects in cities. However, their community composition may change with increased urbanization. As our results showed, exotic species such as mosquitoes may dominate the communities in these habitats. In the case of vector species, high abundances may affect human and animal health via increased pathogen transmission. Therefore, we suggest raising awareness about potential risks of these habitats and possible measures preventing the establishment and spread of harmful species, while still supporting native biodiversity in urban spaces.