Dengue in Paraguay is an endemic disease of public health importance. Several studies suggest that an increased density of Aedes aegypti and the presence of dengue cases may be associated with climatic conditions. This study aimed to establish the phenotypic variations of Ae. aegypti from four cities (Asunción, Itauguá, Minga Guazú, and Ciudad del Este) and the potential association of environmental variables with the number of eggs in capture sites. Eleven morphometric phenotypic characters were evaluated, and environmental data were obtained from Earth Engine and local meteorological stations. An analysis was carried out using principal component analysis and linear discriminant analysis, and we estimated the correlation using [relative humidity, Normalized Difference Vegetation Index (NDVI) and Normalized Difference Water Index (NDWI)] between variables and the number of eggs in each site. Differences in mean NDVI and NDWI between cities and their relationship with the morphometric performance of individuals were also assessed. The study demonstrated morphometric variations between the populations of Ae. aegypti from two ecoregions, with the Litoral ecoregion populations presented a greater phenotypic variation than those observed in the Alto Paraná ecoregion. Significant statistical associations were registered between the number of eggs with relative humidity (r = -0.45) and the NDVI at 100 meters from the capture points (r = -0.61) for Minga Guazú, and with the NDWI at 100 meters (r = 0.54) for Ciudad del Este. Future studies on these Ae. aegypti populations, and its dispersion could contribute to improve vector control measures and foster future genetic studies.