Arboviruses transmitted by Aedes aegypti (e.g., dengue, chikungunya, Zika) are of major public health concern on the arid coastal border of Ecuador and Peru. This high transit border is a critical disease surveillance site due to human movement-associated risk of transmission. Local level studies are thus integral to capturing the dynamics and distribution of vector populations and social-ecological drivers of risk, to inform targeted public health interventions. Our study examines factors associated with household-level Ae. aegypti presence in Huaquillas, Ecuador, while accounting for spatial and temporal effects. From January to May of 2017, adult mosquitoes were collected from a cohort of households (n = 63) in clusters (n = 10), across the city of Huaquillas, using aspirator backpacks. Household surveys describing housing conditions, demographics, economics, travel, disease prevention, and city services were conducted by local enumerators. This study was conducted during the normal arbovirus transmission season (January - May), but during an exceptionally dry year. Household level Ae. aegypti presence peaked in February, and counts were highest in weeks with high temperatures and a week after increased rainfall. Presence of Ae. aegypti was highly variable between clusters. Hierarchical generalized linear models were used to explore household social-ecological variables and female Ae. aegypti presence. Houses with Ae. aegypti used larvicide in water tanks and had high awareness of dengue transmission. We found that homes were more likely to have Ae. aegypti when heads of household had lived in the neighborhoods for longer than average (>22 years), when households had more occupants than average (>4.5), had a female head of household, and received more frequent garbage collection. Ae. aegypti presence was less likely in households with reliable water supply and septic systems. Based on our findings, infrastructure access, urban occupancy patterns, and seasonal climate are important considerations for vector control in this city, and even in dry years, this arid environment supports Ae. aegypti breeding habitat.Author summaryMosquito transmitted infectious diseases are a growing concern around the world. The yellow fever mosquito (Aedes aegypti) has been responsible for recent major outbreaks of disease, including dengue fever and Zika. This mosquito prefers to bite humans and lay its eggs in artificial containers such as water tanks and planters. This makes Ae. aegypti well suited to become established in growing urban areas. Controlling these mosquitoes has been an important way to reduce the risk of disease transmission. Studies that are undertaken to understand local factors that contribute to the continued survival of the mosquito can be used to inform control practices. We conducted a study in the largest city on the border of Ecuador and Peru where we collected adult mosquitoes from houses and surveyed household members about their behaviors, perceptions, and housing infrastructure associated with the mosquito vector. Mosquitoes were most numerous in weeks with high temperatures and a week after increased rainfall. Larvicide was a commonly used control strategy in homes where Ae. aegypti was present. We found that houses that had more people, female heads of household, heads of household that had lived in the neighborhood for a long time, and had unreliable water service, were more likely have mosquitoes present, while houses that used septic systems were less likely to have mosquitoes present.