Several sediment cores from the Pearl River Delta were collected to investigate the relationship of trace metal contamination with algae-derived organic matter in the last 50 years. Trace metals were analyzed with ICP-MS, and algal organic matter (AOM) was measured with Rock-Eval pyrolysis. It was found that Cu, Zn, Ag, Cd, and As were elevated in the last three decades from three reservoirs, while all of the target metals showed no significant enrichment in estuarine sediment cores. Cu, Cr, Co, Cd, Zn, Ag, Ni, As, and Mn normalized to Ti were strongly associated with AOM in the sediments of eutrophic reservoirs, suggesting that AOM played an important role in controlling the accumulation of trace metals. Principal component analysis (PCA) and enrichment factor (EF) were also used to assess the enrichment of trace metals. The above result indicated that the sedimentary process of As, Cd, Cu, Zn, Ni, Cr, Co, Ag, and Mn was significantly affected or/and controlled by primary productivity in eutrophic, non-point polluted reservoirs.