Mosquitoes and mosquito-borne pathogens within urban regions may vary in response to short-term spatial and temporal changes in climate, as well as the distribution of water bodies, habitats and wildlife. Predicting where and when mosquito-borne pathogens are likely to occur is vital to safeguarding against outbreaks of human disease and developing strategic mosquito management programs. The aims of our study were to determine: 1) the spatial and temporal variability in mosquito communities over the late summer and early autumn in a metropolitan region; and, 2) the presence of arboviruses in the various mosquito species at the sites and the implications for mosquito-borne disease risk. Mosquito populations were sampled, and tested for the presence of arboviruses, using a replicated CO2 trap sampling design to determine the spatial and temporal variability in mosquito communities over the late summer and early autumn in the metropolitan region of Sydney, Australia. Eleven sites were classified as highly urban, suburban or estuarine, based on the water habitats present and distance from the central business district. Mosquito community composition within metropolitan urban regions was not significantly different from those in suburban areas with nearby bushland. However, areas associated with estuarine wetlands recorded significantly different mosquito fauna and a higher abundance of mosquitoes. Stratford virus was the only arbovirus detected in the study and was detected at a higher incidence at the three estuarine sites. This mosquito-borne pathogen is considered of only minor public health concern and while more hazardous viruses were not detected, the high abundance of known vector mosquito species highlights the potential risk and suggests the need for annual surveillance to assist local health authorities mange these risks. Our findings highlight the importance of considering estuarine areas separately when assessing the risk of mosquito-borne disease. This is critical for many cities globally, as important population centres are often located in coastal areas adjacent to estuarine wetlands.