Fish communities from two lagoon ecosystems, Ria Formosa (Portugal) and Grand Cul-de-Sac Marin (Guadeloupe), show interesting similarities of spatial and temporal organization. On the temporal scale, three community changes are observed in both systems, corresponding to massive arrivals and/or departures of migratory species. However, these migrations are more conspicuous in the Ria Formosa than in the Grand Cul-de-Sac Marin. On a spatial scale, the community structure is also largely determined by migratory species, whose abundance is a factor of homogenization. This is clearly observed in Ria Formosa, where the lagoon selection applies on a regional scale. Conversely, the community of sedentary fish identifies remarkable stations affected by chronic aggressions such as tourism or pollution. An explicative analysis, comprising a discriminant analysis and multiple regressions was realized on the data collected in the Grand Cul-de-Sac Marin. This analysis made it possible to determine the important environmental descriptors in the two complementary processes involved in recruitment: migrant availability, which determines the temporal organization of the fish assemblage. These migrations are explained by water temperature and salinity, two descriptors controlled by climatic conditions; the settlement process, which determines the spatial organization of the fish assemblage. This is explained by habitat descriptors such as visibility and turtlegrass blade length, or trophic descriptors, such as primary production, zooplankton density or nitrate concentration.