The diversity patterns of the polychaete fauna from a Pacific coastal lagoon were described. Polychaetes were collected in 1995 and 1998. This lagoon is formed by 2 arms: the western arm named Bahia Falsa and the eastern arm named Bahia San Quintin. 46 stations were sampled with a geological box corer. A total of 3,275 polychaetes, 28 families, 56 genera, and 104 species were identified in 1995, and 3,168 polychaetes were collected in 1998, 21 families, 39 genera and 65 species. From all the macrofauna collected in both surveys, polychaetes represented 45.2%. From the species collected, 55% correspond to new records for the area. Families Dorvilleidae, Polynoidae, Oweniidae, Scalibregmatidae, Sternapsidae and Sigalionidae present in 1995, were not in 1998 survey. The stations with higher abundances (. 100 specimens/0.02 m2) were located on the southern half of Bahia San Quintin. Species richness and diversity were also higher in San Quintin Bay. From the 30 families previously reported for San Quintin lagoon, 23 have been collected and 6 families were added: Ampharetidae, Oweniidae, Scalibregmatidae, Sternapsidae, Dorvilleidae and Sigalionidae. Families not found in both surveys were: Paraonidae, Magelonidae, Apistobranchidae, Sphaerodoridae, Trichobranchidae, Chrysopetalidae and Arenicolidae. Results showed slightly lower redox potential values (2336 to 1187 mV), slightly higher sediment temperatures (19.88–22.18C) and organic matter contents (0.3–4.1%) in 1998. From 1995 to 1998 a change in the composition and structure of the polychaete communities was noted; species richness diminished from 104 to 65 species. The trophic complexity changed with an increase of deposit-feeders, the abundance of other trophic categories decreased, indicating a loss of complexity. Significant changes in the abundance of some families were detected, some increased their abundances: Spionidae from 17% to 48%, Orbiniidae from 4% to 13%; other families decreased in terms of abundance and number of species: Lumbrinereidae from 11% to 1.4%, Nereididae from 9% to 1% and Sabellidae from 14% to 5%. These modifications altered the composition and structure of the polychaete communities in this lagoon. Increased anthropogenic disturbance (oyster culture, agriculture) and environmental variability due to the ENSO 97–98 may have affected recruitment and survival of some polychaete species.