Mercury (Hg), six alkyl esters of p-hydroxybenzoic acid (parabens), and their metabolite, 4-hydroxybenzoic acid (PHBA), were simultaneously studied in sediments from the upper Huai River, Henan Province, China. There were higher concentrations of Hg in the surface sediments from the Huai River during the moderate precipitation season (MPS^②) as compared to the minimal precipitation (MPS^①) and high precipitation seasons (HPS), and as compared to core sediments. The Hg values in all sediments were above the background value. The Hg contents in the tributaries were much higher than those in the mainstream. The concentrations of ∑parabens in the core sediments ranged from 2.45 to 22.2 ng/g while the concentrations of PHBA ranged from 11.3 to 155 ng/g. Methylparaben (MeP) and propylparaben (PrP) were the most commonly detected parabens. Total organic carbon (TOC) and black carbon (BC) played important roles in the distribution of Hg in the surface sediments during the minimal precipitation and high precipitation seasons and affect the distribution of Hg and parabens in core sediments. Sand (>63 μm) was another factor affecting the distribution of Hg and parabens in core sediments. The concentrations of PHBA and Hg in core sediments were positively correlated. Temporal records of Hg and parabens in core sediments reflected local social changes. Hg content in the surface sediments during the MPS^② was associated with relatively high ecological risks while parabens in the core sediments were associated with low level risks.