Nonpoint source pollution (NPS) such as stormwater runoff may introduce high loads of bacteria, impairing surface water bodies. The existing filter materials in stormwater best management practices (BMP) are typically not designed to inactivate bacteria. Herein, novel filtration media were extensively tested for microbial load reduction in stormwater runoff. Red cedar wood chips (RC) were amended with different loadings of either 3-(trihydroxysilyl) propyldimethyloctadecyl ammonium chloride (TPA) or silver nanoparticles (AgNP). Under batch conditions at 25 °C, log10 removal values (LRV) up to 3.71 ± 0.38 (mean ± standard error) for TPA-RC and 2.25 ± 1.00 for AgNP-RC were achieved for Escherichia coli (E. coli), whereas unmodified RC achieved less than 0.5 LRV. Similar trends were observed at 17.5 °C, however at low temperature (10 °C) no statistically significant difference in E. coli inactivation between modified and unmodified RC was detected. Inactivation kinetic studies show that TPA-RC has higher inactivation rate constants compared to AgNP-RC. Under dynamic flow conditions a mass balance approach indicates that even after remobilization up to 99.8% of E. coli removal using 9 mg/g TPA-RC compared to 64.8% for unmodified RC. This study demonstrates that RC wood chips amended with antimicrobial compounds show promising applications as filtration material for the reduction of microbiological contamination load in stormwater runoff.