Pulsed disturbances of larval mosquito sites are likely to have a direct negative effect on mosquitoes but may also have indirect effects due to the alteration of community structure. These altered communities may become attractive to gravid mosquitoes searching for oviposition sites when the disturbances decrease the abundance of mosquito antagonists such as competitors, which often results in an increase in mosquito food resources. However, flash flood disturbances in intermittent riverbeds can also remove mosquito food resources such as algae, so that the net effect of flash floods could be either to increase or decrease mosquito abundance. We conducted an outdoor mesocosm experiment to assess the effects of flash floods on mosquito oviposition habitat selection and larval abundance during the post-disturbance period of community recovery. Mesocosms were artificially flooded. Mosquito oviposition, immature abundance, invertebrate species diversity, chlorophyll a, and abiotic parameters were monitored. Our results showed that the flash flood negatively affected phytoplankton and zooplankton, leading to a decrease of mosquito oviposition in flooded mesocosms compared to non-flooded mesocosms. More broadly, this study indicates how disturbances influence mosquito oviposition habitat selection due to the loss of food resources in ephemeral pools, and it highlights the importance of considering the effects of disturbances in management, habitat restoration, and biodiversity conservation in temporary aquatic habitats.