A citywide control program of Aedes aegypti (L.) (Diptera: Culicidae) mainly based on the use of larvicides reduced infestations but failed to achieve the desired target levels in Clorinda, northeastern Argentina, over 5 yr of interventions. To understand the underlying causes of persistent infestations and to develop new control tactics adapted to the local context, we conducted two pupal surveys in a large neighborhood with ≈2,500 houses and recorded several variables for every container inspected in fall and spring 2007. In total, 4,076 lots and 4,267 containers were inspected over both surveys, and 8,391 Ae. aegypti pupae were collected. Large tanks used for potable water storage were the most abundant and the most productive type of container, accounting for 65–84% of all the pupae collected. Therefore, large tanks were key containers and candidates for improved targeted interventions. Multivariate analysis showed that containers located in the yard, at low sun exposure, unlidded, filled with rain water, and holding polluted water were all more likely to be infested by larvae or pupae. When only infested containers were considered, productivity of pupae was most closely associated with large tanks and rain water. A stochastic simulation model was developed to calculate the expected correlations between pupal and Stegomyia indices according to the characteristics of the distribution of larvae and pupae per container and the spatial scale at which the indices were computed. The correlation between pupal and Stegomyia indices is expected to increase as infestation levels decline.