Studies of the biodiversity of mosquito larval habitats are important for vector-borne disease control programs and help to improve vector distribution maps. This study was designed to investigate the geographical distribution of mosquito species and their larval habitats in urban, rural, and natural areas in northern Spain. Pre-imaginal stages were collected over two sampling periods (spring and summer) in 2019. In the laboratory, immature specimens were reared to the adult stage for species identification by morphological taxonomy and/or molecular methods. In total, 2,182 specimens belonging to 13 different native mosquito species of five genera were collected from 135 sampling points of which 59.2% harbored larvae. Culex pipiens s.l. was the most abundant species (45.1%), followed by Culex torrentium (12.3%), Anopheles maculipennis s.l. (10.2%), Culex hortensis (9.5%), and nine other species with lower frequencies that accounted for less than 25%. By molecular identification, An. maculipennis s.s. was identified as the only species within the An. maculipennis species complex and Cx. pipiens pipiens as the predominant subspecies of the Cx. pipiens species complex. Margins in large sunlit water bodies were the most suitable sites for An. maculipennis s.l., whereas Cx. pipiens s.l. was present in both natural and artificial habitats. The larval site index, species richness, and relative abundance of the mosquitoes were determined based on the characteristics of the sites where they were collected. The public health importance and ecology of some identified mosquitoes is also discussed.