The management of mosquito-borne diseases is a challenge in southern coastal Ecuador, where dengue is hyper-endemic and co-circulates with other arboviral diseases. Prior work in the region has explored social-ecological factors, dengue case data, and entomological indices. In this study, we bring together entomological and epidemiological data to describe links between social-ecological factors associated with risk of dengue transmission at the household level in Machala, Ecuador. Households surveys were conducted from 2014-2016 to assess the presence of adult Aedes aegypti (collected via aspiration) and to enumerate housing conditions, demographics, and mosquito prevention behaviors. Household-level dengue infection status was determined by laboratory diagnostics in 2014-2015. Logistic models and multimodel selection were used to identify social-ecological variables associated with household presence of female Ae. aegypti and household dengue infection status, respectively. We identified significant risk factors for household-level dengue infection reflecting household condition, including bamboo cane construction material, shaded patios, and adjacency to abandoned properties, while housing structures in good condition were identified as protective against dengue infection. Aedes aegypti presence was associated with a greater than average number people per household and interrupted water supply, but was not associated with household level dengue infections. Models of Ae. aegypti presence were unstable, and not well resolved in ranking of competing models, suggesting that highly localized entomological surveillance indicators may not be indicative of risk in communities with hyperendemic dengue fever. These findings add to our understanding of the systems of mosquito-borne disease transmission in Machala, and in the larger region of southern Ecuador, aiding in the development of improved vector surveillance efforts, and targeted interventions.