Twelve bioretention filter columns with different media were designed to study the effects of media on dissolved heavy metals in bioretention systems by changing three test conditions (inflow concentration, discharge ratio, and recurrence interval). The results showed that the average load reduction efficiency of the bioretention soil media (BSM)+10%water treatment residue, BSM+10%green zeolite, and BSM+10%medicinal stone for Cu and Zn was larger than 80%. The highest volume reduction efficiency is 39.25% by BSM+coconut bran. Among the three factors selected in tests, inflow concentration had the biggest degree of influence, followed by discharge ratio and recurrence interval. The media of the upper, middle, and lower layers of each filter column were detected before and after the treatment to study the accumulative characteristics of heavy metals in the bioretention system. The accumulation of Cu, Zn, and Cd in the media of BSM+medicinal stone, BSM+fly ash, BSM+vermiculite, and BSM+turfy soil was relatively low. The contents of the three metals were positively correlated with urease and negatively correlated with protease in the media, but no obvious rule was showed in the accumulation of dissolved heavy metals with depth.