To prevent the risk of mosquito-borne disease outbreaks, larval source management remains the most sustainable and effective mosquito control strategy. The present study aimed to determine the influence of environmental characteristics of mosquito larval habitats in an urban area of Marseille, France. Fourteen sites containing water were monitored every 2 weeks from May to October 2015 for mosquito species occurrence and larval density, and environmental parameters were measured at each visit. Rapid and accurate species identification of mosquito larvae was performed using an innovative MALDI-TOF MS method. A total of 6753 larvae (L1–L4) and pupae were collected, of which 35.8% (n = 2418) were speciated using MALDI-TOF MS. Correct identifications were obtained for 2259 specimens (93.4%). A total of five mosquito species were found, including Aedes (Ae.) albopictus, Culex (Cx.) p. pipiens, Cx. hortensis, Cx. impudicus, and Culiseta (Cs.) longiareolata. Larvae of the Culex genus were predominant in both density and distribution. Small, shaded pools of shallow water favored Ae. albopictus colonization, whereas the wide distribution of Cx. p. pipiens demonstrated that this species was weakly influenced by environmental changes. The present work confirms that MALDI-TOF MS is a useful tool for mosquito speciation and suggests that understanding the environmental factors associated with the occurrence and density of mosquito species at the larval stage in Marseille may aid in the future implementation of mosquito control programs.