In Terminos Lagoon, Mexico, more than 80 fish species use the mangrove and seagrass habitats. We studied nekton dynamics in an inlet seagrass system and a more sheltered seagrass/mangrove system located behind a barrier island. Seasonal community biomass ranges from 0.6 to 5.2 g wet wt m-2. For the two habitats together, there are 28 dominant species. Eleven species were common to both areas: Sphoeroides testudineus (Linnaeus, 1758), Archosargus rhomboidalis Linnaeus, 1758, A. probatocephalus (Walbaum, 1792), Arius felis (Linnaeus, 1766), A. melanopus (Gunther, 1864), Eucinostomus gula (Cuvier & Valenciennes, 1830), Bairdiella chrysoura (Lacepede, 1803), Orthopristis chrysoptera (Linnaeus, 1766), Chilomycterus schoepfi (Walbaum, 1792), Opsanus beta (Goode & Bean, 1879) and Lutjanus griseus (Linnaeus, 1758). Ten species used exclusively the inlet seagrass system: Urolophus jamaicensis (Cuvier, 1817), Haemulon aurolineatum (Cuvier, 1829), H. bonariense (Cuvier, 1830), H. plumieri (Lacepede, 1802), Anisotremus virginicus (Linnaeus, 1758), Odontoscion dentex (Cuvier, 1830), Corvula sanctae-luciae (Jordan, 1890), Nicholsina usta (Valenciennes, 1839), Stephanolepis hispidus (Linnaeus, 1766) and Diodon hystrix Linnaeus, 1758. Seven species were dominant only in the seagrass/mangrove system: Anchoa mitchilli (Cuvier & Valenciennes, 1848), Scorpaena plumieri Bloch, 1789, Cynoscion nebulosus (Cuvier & Valenciennes, 1830), Diapterus rhombeus (Cuvier & Valenciennes, 1830), Bairdiella ronchus (Cuvier & Valenciennes, 1830), Cichlasoma urophtalmus (Gunther, 1862) and Acanthostracion quadricornis (Linnaeus, 1758). Comparative analysis showed that periodic variation in biomass and diversity of fish assemblages in seagrass and seagrass/mangrove habitats were synchronized with sizes and densities of population, season of the year (dry, wet, ‘nortes’), circulation pattern, and patterns of primary production (phytoplankton, Thalassia testudinum Konig, 1805; and Rhizophora mangle Linnaeus). This analysis allowed the definition of 3 life-cycle patterns with a clear nektonic ‘seasonal programming’ following the timing of primary production in these critical habitats: (1) marine species which spawn in or near the inlet with eggs and larvae transported into and distributed throughout the lagoon by the predominant currents; (2) estuarine-marine species which spawn in different habitats of the lagoon and use the seagrass/mangrove system as a nursery area, and (3) species which complete their life history in the inlet seagrass and/or seagrass/mangrove systems.