The aim of this study was to describe and analyze the structure, distribution, and temporal variation in the composition of benthic polychaeta and their relation to abiotic characteristics in marine sediments along the continental shelf of Bahia de Todos Santos, Baja California, Mexico. Benthic macrofauna and environmental variables were collected to coordinated with a long-term ocean monitoring project known as the Southern California Bight Regional Monitoring Program. A total of nineteen stations were collected in September 1998, twenty stations in November 2003, fifteen stations in December 2013 and sixteen stations in September 2018. These data were compared to assess the response of benthic polychaete assemblages to natural and human induced changes in sediment characteristics. All stations were sampled using a Van Veen grab (0.1 m2) at depths between 15 to 206 m. Sites were selected using a multiple density nested random-tessellation stratified design. Environmental parameters measured included depth (m), sediment grain size <63µm (%), organic carbon (%), and concentration of metals: Co, Cd, Cr, Cu, Fe, Mn, Ni, Pb, and Zn. A total of 11,854 polychaetous annelids were identified in 43 families, with the numerically dominant families for all years (Spionidae, Chaetopteridae, Cirratulidae, Maldanidae, Onuphidae, and Ampharetidae) accounting for 52.95% of individuals. The best represented families in 1998 were Spionidae, Maldanidae, Ampharetidae and Cirratulidae. In 2003 the best represented families were Spionidae, Maldanidae, Cirratulidae, and Onuphidae; in 2013 Chaetopteridae and Spionidae; and in 2018 Spionidae, Ampharetidae, Syllidae and Cirratulidae. The Bio-Env multivariate analysis showed that the factors that most correlated with the abundance and richness of families and had the greatest influence over spatial distribution trends for community structure were %Organic carbon and Cu concentration during 1998, % Organic carbon and depth in 2003 and Pb concentration in 2013.