In this work, novel adsorbents based on 3D hierarchical silica monoliths functionalized with thiol groups were used for the removal of Hg(II) ions from an acidic aqueous solution (pH 3.5). Silica monoliths were synthesized by using two different pluronic triblock polymers (P123 and F127) to study the effect of porous structure on their sorption capacity. Before and after functionalization by grafting with 3-mercaptopropyltrimethoxysilane (MPTMS), the monoliths were characterized by several techniques, and their Hg(II) removal potential was evaluated in batch experiments at 28 °C and pH 3.5, using different initial concentrations of Hg(II) ions in water (200–500 mg L−1). The thiol groups of the monoliths calcined at 550 °C showed thermal stability up to 300 °C (from TG/DTG). The functionalized monolith synthesized with P123 polymer and polyethylene glycol showed favorable hierarchical macro-mesopores for Hg(II) adsorption. M(P123)–SH exhibited 97% removal of Hg(II) at concentration 200 mg L−1. Its maximum adsorption capacity (12.2 mmol g−1) was two times higher than that of M(F127)–SH, demonstrating that the 3D hierarchical macro-mesoporosity allowing accessibility of Hg(II) to thiol groups favors the physical and chemical adsorption of Hg(II) under slightly acidic conditions.