Background Outbreaks of dengue fever caused by viruses transmitted by Aedes aegypti mosquitoes are repeatedly reported in West Africa. Burkina Faso has experienced major dengue outbreaks most notably in 2016 and 2017, with 80% of cases recorded in Ouagadougou (Central health region). In order to better understand the ecology of this vector to provide information for control, a study on the productivity of Aedes breeding sites measured by abundance of immature stages, and resultant adult body size, and breeding site characteristics was undertaken in three Health Districts (Baskuy, Bogodogo, and Nongremassom) of the city of Ouagadougou. Methods Adult mosquitoes were collected indoors and outdoors in 643 households during the rainy season from -month- to -month- 2018. Water containers were systematically recorded and prospected for larval presence or absence. Breeding container characteristics including size, temperature, pH and conductivity were recorded as well as water volume. Traditional Stegomyia indices were calculated; generalised mixed models were fitted to larval and pupal densities, and the contribution of each covariate to the model evaluated by the Z-value and associated P-value. Results A total of 1,061 breeding sites were inspected, of which 760 were positive for Aedes aegypti immature stages. Tires, medium (Buckets/Cans/Pots) and large (Bin/barrel/drums) containers were the most frequent, positive and productive larval habitats in each health district. Of the Stegomyia indices, the Breteau, house and container indices exceeded WHO dengue risk thresholds. Generalised Linear Mixed Models (GLMMs) showed that larval and pupal abundances were each associated with container type, physicochemical characteristics and collection month, but with significant differences among container types among health districts. Aedes aegypti body size was positively associated with containers type, diameter, electrical conductivity; and negatively associated with pH, temperature, and a containers’ level of exposure to sunshine. Conclusion We provide data on putative determinants of Aedes aegypti immature habitat productivity, which are useful to better understand Aedes aegypti proliferation. The results suggest that targeting the most productive containers could contribute to dengue vector control strategies in Burkina Faso.