Environmental disturbance may have direct and indirect impacts on organisms. We studied the colonization of ephemeral water bodies by mosquitoes (Diptera: Culicidae) in the Wheatbelt region of southwest Western Australia, an area substantially affected by an expanding anthropogenic salinization. Mosquitoes frequently colonized ephemeral water bodies, responded positively to rainfall, and populated smaller water bodies more densely than larger water bodies. We found that the habitat characteristics of ephemeral water bodies changed in association with salinity. Consequently relationships between salinity and abundance of colonizing mosquitoes were direct (salinity—mosquito) and indirect (salinity—water body characteristics—mosquito). Overall, the structure of mosquito assemblages changed with increasing salinity, favoring an increased regional distribution and abundance of Aedes camptorhynchus Thomson (Diptera: Culicidae), a vector of Ross river virus (RRV; Togoviridae: Alphavirus). We conclude secondary salinization in the Western Australia Wheatbelt results in enhanced vectorial potential for RRV transmission.