Seasonal meroplankton abundances of Köyceğiz-Dalyan Lagoon System were examined in this study. Also, changes in the diversity and abundance of meroplanktonic larvae because of the different two salinity layers of the system were investigated. Meroplankton samples were taken by Unesco standart plankton net with 200 micrometer mesh size horizontally from three stations. Temporal and spatial differences in the abundance of meroplankton groups were examined by permutational multivariate analysis of variance (PERMANOVA). Environmental parameters which are temperature, salinity and dissolved oxygen were measured from the surface. Meroplankton groups of the study area were nauplius, zoea, cyprid larva, stomatopod larva, hydrozoan larva, ephyra, polychaeta larva, fish egg, fish larva and gastropod larva. Meroplankton and holoplankton abundances showed two peaks in April and October. There were statistically significant differences in the abundance of meroplankton amongst seasons especially between summer-winter and winter-spring. In October and November Mediterranean water enters the Köyceğiz-Dalyan Lagoon System through the bottom of the system, whereas in winter and spring, the lagoon and coastal zone were under the influence of Lake Köyceğiz.