Using activated carbon (AC) as thin layer capping to reduce mercury (Hg) released from contaminated sediment is a feasible and durable remediation approach. However, several aqueous factors could greatly affect the Hg fate in the aquatic system. This study thus intends to clarify the influences on Hg adsorption by AC with the presence of sulfide, dissolved organic matter (DOM), and chloride. The lab-scale batch experiments were divided into two parts, including understanding (1) AC adsorption performance and (2) Hg distribution in different phases by operational definition method. Results showed that the Hg adsorption rate by AC was various with the presence of sulfide, chloride, and DOM (from fast to slow). Hg adsorption might be directly bonded to AC with Hg-Cl and Hg-DOM complexes and the rate was mainly controlled by intraparticle diffusion. In contrast, “Hg + sulfide” result was better described by pseudo-second order kinetics. The Hg removal efficiency was 92–95% with the presence of 0–400 mM chloride and approximately 65–75% in the “Hg + sulfide” condition. Among the removed Hg, 24–29% was formed into aqueous-phase particles and about 30% Hg was adsorbed on AC with 2–20 μM sulfide. Increasing DOM concentration resulted in more dissolved Hg. The proportion of dissolved Hg increased 31% by increasing DOM concentration from 0.25 to 20 mg C L− 1. Simultaneously, the proportion of adsorbed Hg by AC decreased by 47%. Overall, the presence of chloride increases the Hg adsorption by AC. In contrast, the presence of sulfide and DOM causes a negative effect on AC adsorption.