The accelerating rate of outbreaks from mosquito borne diseases are urging the development of updated and effective tools for the surveillance of insect populations and their larval habitats. Harmonized field protocols help to build a comprehensive picture on species-specific vector ecology and generate important knowledge for implementing coordinated mosquito surveillance programs at regional scales and across continents. In this study, we test the efficiency and potential barriers of available harmonized protocols from earlier EU project VectorNet. As a kind of litmus test for such protocols, we specifically aim to capture the ecoregional variation of breeding site characteristics and population density of five mosquito vectors in Europe and Africa. As expected, the five species considered show different aquatic habitat preferences. Culex pipiens, Aedes albopictus in Europe and Ae. aegypti in Africa select breeding habitats within specific volume classes, while Anopheles gambiae and An. coluzzii may select breeding habitats based on seasonal availability. Population densities in aquatic habitats greatly varied across species and countries, but larval production sites of Ae. albopictus generate populations with higher ratio of pupae compared to the other species. This result underlines the fundamental ecological difference between the selected vector species disregarding of the ecoregion. Mean water temperatures had limited variation across species and higher among countries. Understanding the ecology of native and non-native mosquito vectors is key in evaluating transmission risks for diseases such as West Nile, chikungunya and dengue fevers, zika and malaria. The available harmonized field protocols are a valuable tool for achieving homogeneous mosquito surveillance in Europe and Africa.