Green roofs (GRs) are a widely recognized green infrastructure (GI) strategy that helps reduce runoff volume and runoff pollution caused by the significant increase in impervious urban areas. However, the leaching of several nutrients from GR substrates is a growing concern. Biochar, a carbon-rich material, possesses advantageous properties that can help address such environmental challenges associated with GRs. Therefore, this paper aimed to undertake a field study to investigate the impacts of various biochar application methods, particle sizes, and amendment rates on the quality of runoff from GRs. Observational data of runoff quality were collected over a two-month period from five newly established 1 m × 1 m biochar-amended GR test beds and a control test bed without biochar, with all test beds subjected to artificially simulated rainfall. The results indicated that the addition of biochar did not result in a significant improvement in runoff pH, whereas the electrical conductivity (EC) was higher in runoff from GRs with biochar-amended substrates. When comparing the total nitrogen (TN) concentration in runoff from the non-biochar GR (ranging from 3.7 to 31 mg/L), all biochar test beds exhibited higher TN release (4.8 to 58 mg/L), except for the bed where medium biochar particles were applied at the bottom of the substrate (ranging from 2.2 to 21 mg/L). Additionally, all biochar-amended GRs exhibited higher TP concentrations in runoff (0.81 to 2.41 mg/L) when compared to the control GR (0.35 to 0.67 mg/L). Among the different biochar setups, GR with fine biochar particles applied to the surface of the substrate had the poorest performance in improving runoff water quality. Despite these mixed results, biochar holds significant potential to improve runoff quality by significantly increasing water retention, thereby reducing pollutant loads.