Sediment cores were collected in urban (0–50 cm), rural (0–40 cm) and reclamation-affected river (0–40 cm) environments in the Pearl River Delta. Concentrations of 16 organochlorine pesticides (OCPs) were determined in all collected samples to identify the depth-distribution, possible sources and ecotoxicological risks of OCPs in river sediments affected by urbanization and reclamation in a Chinese delta. The results showed that the top 10 cm of rural river sediments had slightly lower concentrations of the 16 OCPs compared to urban and reclamation-affected rivers, whereas the 30–40 cm sediment layers in the rural river showed higher levels of the 16 OCPs. However, higher OCPs levels were observed in the 20–30 cm sediment layers in the urban river than in the rural and reclamation-affected rivers. The principal OCPs in most deeper sediment layers were hexachlorobezene (HCB), the combination of aldrin, endrin and dieldrin (ΣDRINs) and the combination of α-HCH, β-HCH and γ-HCH (ΣHCHs). The predominant OCPs in surface sediments were HCB, ΣDRINs and the combination of p,p’-DDD, o,p’-DDT, p,p’-DDT and p,p’-DDE (ΣDDTs). Generally, OCP concentrations decreased with depth along sediment profiles at most sampling sites in the three types of rivers. The source analyses indicated that some sampling sites were still suffering from the recent use of hexachlorocyclohexanes (HCHs), dichlorodiphenyltrichloroethanes (DDTs) and aldrin. According to the soil quality thresholds of China, the levels of HCHs and DDTs at most sampling sites were below class Ⅰ criteria. Based on the sediment quality guideline quotient (SQGQ), the combined ecotoxicological risk of OCPs (γ-HCH, dieldrin, p,p'-DDD, p,p'-DDE and p,p'-DDT) in surface sediments (0–10 cm) was higher than deeper sediments, and the rural river sediments exhibited a higher combined ecotoxicological risk than the sediments in urban and reclamation-affected rivers.