These data were collected as a component of a year-long study examining the seasonal occupancy and distribution of the southern house mosquito Culex quinquefasciatus in Kīpahulu Valley, Haleakalā National Park, which is critical habitat for two endangered Maui endemic forest birds. As a vector of the avian malaria parasite Plasmodium relictum, Culex quinquefasciatus is a key limiting factor of endemic Hawaiian forest birds. The data collected in this study complements a larger study that included adult mosquito monitoring to document the altitudinal distribution, seasonal occurrence, relative abundance of adult mosquitoes, and stream surveys to determine the larval habitat availability and prevalence of larval mosquitoes. Environmental DNA (eDNA) may be used as a non-invasive surveillance tool to complement traditional mosquito monitoring techniques, potentially providing a broader window of time to assess whether mosquito larvae had recently emerged from ephemeral water sources despite the lack of visual confirmation. 195 water samples, including negative controls, were taken in the field from a variety of water sources in two primary locations, Delta and Palikea Camps, within native forests of Kipahulu Valley Maui, during 2022 and 2023. Water sources included those with visible mosquito larvae of two species, Culex quinquefasciatus and Aedes japonicus. eDNA was collected from water sources using three different filtering techniques and filter types. Data describing the sampling conditions was collected such as source dimensions, depth at which water was filtered, substrate type, and volume of water filtered.