The physicochemical flux, composition and abundance of crustacean larvae in two mesohaline creeks of Lagos Lagoon were investigated. The status of the Physico-chemical parameters indicates a non-significant difference between variables except Alkalinity with Abule-Eledu Creek having significantly higher mean value (144.4±2.2 mg/L) than Abule-Agege Creek (121.9±4.9 mg/L). The transparency values of the creeks increased with a reduction in the amount of rainfall while the water temperature as well as salinity values increased appreciably with the dry season. An increase in conductivity (>190.40 μS/cm) and salinity (>10.50‰) in the dry months for both creeks was also observed. The crustacean larvae were represented by five orders with Calanoida and Cyclopoida (Sub-Class: Copepoda) were the most frequent and notable orders occurring in Abule-Eledu and Abule-Agege creeks respectively. Other crustacean categories such as Mysida, Calanoida and Harpaticoida were also recorded. Total species diversity was14 in Abule-Eledu creek and 17 in Abule-Agege Creek. Shannon-Wiener Index values ranged between 0.90 and 0.96 for Abule-Eledu Creek and between 0.97 and 1.09 for Abule-Agege Creek. With the exception of Menhinick Index and Equitability Index, all other biotic indices were higher in Abule-Agege Creek than Abule-Eledu creek. This study therefore suggests that Calanoida and Cyclopoida which are orders of the subclass Copepoda are the dominant crustacean zooplankton group in the creeks of the Lagos Lagoon