Stormwater control measures (SCMs) are essential to manage runoff in urban areas. Mussel shell waste has been recently proposed as sustainable treatment media in SCM to remove metals from runoff. In this study, a group of laboratory-scale column experiments were conducted to investigate the use of crushed mussel shell waste to remove dissolved zinc from actual roof runoff during different filtration flow rates (1, 3, 5, 10 L/min). Heat-treated mussel shells (TMS) and untreated mussel shells (UTMS) were utilized as treatment media with two column depths (1.0 m and 0.8 m). The microstructures and chemical characteristics of TMS and UTMS were examined by using a group of Scanning Electron Microscopy (SEM) and Energy Dispersive X-ray Spectroscopy (EDS) tests before and after the filtration process, and water samples were analyzed by using an Inductively Coupled Plasma Mass Spectrometry (ICP-MS) instrument. TMS and UTMS showed consistent high removal efficiency for dissolved zinc with (>98%) efficiency during 1 L/min filtration rate. The average removal performance was estimated at >94% and >82% for the 1.0 m and 0.8 m column depths of TMS media, and >92% and >72% for the 1.0 m and 0.8 m depths of UTMS media, respectively. The heat treatment improved the removal of zinc with significant statistical difference (i.e. p < 0.05) during short contact times (0.8 m depth, and high filtration rates). Mussel shell waste showed practical removal performance of zinc even during high filtration rates (>5 L/min). Mussel shell waste showed potential benefits as a sustainable and cost-effective filtration media for removal of dissolved zinc in future stormwater systems.