BackgroundArbovirus diseases such as dengue, Zika, and chikungunya are a public health threat in tropical and subtropical areas. In the absence of a vaccine or specific treatment, vector management (in this case the control of the primary vectorAedes aegypti)is the best practice to prevent the three diseases. A good understanding of vector behaviour, ecology, human mobility and water use can help design effective vector control programmes. This study collected baseline information on these factors for identifying the arbovirus transmission risk and assessed the requirements for a large intervention trial in Colombia.MethodsBaseline surveys were conducted in 5,997 households, randomly selected from 24 clusters (neighbourhoods with on average 2000 houses and 250 households inspected) in the metropolitan area of Cucuta, Colombia. The study established population characteristics including water management and mobility as well as larval-pupal indices which were estimated and compared in all clusters. Additionally, the study estimated disease incidence from two sources: self-reported dengue cases in the household survey and cases notified by the national surveillance system.ResultsIn all 24 study clusters similar social and demographic characteristics were found but the entomological indicators and estimated disease incidence rates varied. The entomological indicators showed a high vector infestation: House Index = 25.1%, Container Index = 12.3% and Breteau Index = 29.6. Pupae per person Index (PPI) as an indicator of the transmission risk showed a large range from 0.22 to 2.04 indicating a high transmission risk in most clusters. The concrete ground tanks for laundry –mostly outdoors and uncovered- were the containers with the highest production ofAe. aegyptias 86.3% of all 17,613 pupae were identified in these containers. Also, the annual incidence of dengue was high: 841.6 self-reported cases per 100,000 inhabitants and the dengue incidence notified by the National surveillance system was 1,013.4 cases per 100,000 in 2019. Only 2.2% of the households used container water for drinking. 40.3% of the study population travelled during the day (whenAedesmosquitoes bite) outside their clusters.ConclusionsThe production ofAe. aegyptimosquitoes occurred almost exclusively in concrete ground tanks for laundry (lavadero), the primary intervention target. The baseline study provides necessary evidence for the design and implementation of a cluster randomized intervention trial in Colombia.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12889-023-15893-4.