A temporal analysis of the benthic polychaete community and its relationship with environmental variables was conducted by comparing coastal sediment samples collected in three separate sampling events between 1998 and 2013 from the southern end of the Southern California Bight (SCB). Environmental variables indicated a spatio-temporal increase of the sand fraction in sediment composition. Station stratification by depth from shallow to deep, and a reduction of trace metal enrichment (Co, Cr, Cu, Mn, Ni, Pb and Zn) was also found. There was a notable change in polychaete family composition due to high abundances and frequency of Spionidae, Chaetopteridae and Phyllodocidae in 2013, especially close to the Binational wastewater treatment plant discharge. An increase in polychaete abundance, richness and diversity was indicative of a probable relationship with regional weather conditions (El Niño-Southern Oscillation and recent drought events during sampling) along with local anthropogenic discharges of wastewater treatment plants in the area.