Dengue incidence continues to increase globally and, in the absence of an efficacious vaccine, prevention strategies are limited to vector control. It has been suggested that targeting the most productive breeding sites instead of all water-holding containers could be a cost-effective vector control strategy. We sought to identify and continuously control the most productive Aedes (Stegomyia) breeding site in an endemic urban area in Colombia and followed the subsequent incidence of dengue. In the urban area of Guadalajara de Buga, southwestern Colombia, potential breeding sites inside and outside houses were first characterized, and local personnel trained to assess their productivity based on the pupae/person index. Simultaneously, training and monitoring were implemented to improve the dengue case surveillance system. Entomological data and insecticide resistance studies were used to define the targeted intervention. Then, a quasiexperimental design was used to assess the efficacy of the intervention in terms of the positivity index of the targeted and non-targeted breeding sites, and the impact on dengue cases. Street catch basins (storm drains) were the potential breeding site most frequently found containing Aedes immature stages in the baseline (58.3% of 108). Due to the high resistance to temephos (0% mortality after 24 h), the intervention consisted of monthly application of pyriproxyfen in all the street catch basins (n = 4800). A significant decrease in catch basins positivity for Aedes larvae was observed after each monthly treatment (p < 0.001). Over the intervention period, a reduction in the dengue incidence in Buga was observed (rate ratio 0.19, 95% CI 0.12-0.30, p < 0.0001) after adjusting for autocorrelation and controlling with a neighboring town, Palmira, This study highlights the importance of street catch basins as Aedes breeding sites and suggests that their targeted control could help to decrease dengue transmission in such areas.