The aim of the study is to assess the influence of drainage layer made of reactive material Polonite® on the water retention and P-PO4 concentration in runoff. A column experiment was performed for extensive substrate underlined by 2 cm of Polonite® layer (SP) and the same substrate without supporting layer as a reference (S). The leakage phosphorus concentration ranged from 0.001 to 0.082 mg P-PO4·L−1, with average value 0.025 P-PO4·L−1 of S experiment and 0.000–0.004 P-PO4·L−1 and 0.001 P-PO4·L−1 of SP experiment, respectively. The 2 cm layer of Polonite® was efficient in reducing P outflow from green roof substrate by 96%. The average effluent volumes from S and SP experiments amounted 61.1 mL (5.8–543.3 mL) and 46.4 mL (3.3–473.3 mL) with the average irrigation rate of 175.5 mL (6.3–758.0 mL). The substrate retention ability of S and SP experiments was 65% and 74%, respectively. Provided with reactive materials, green roof layers implemented in urban areas for rain water retention and delaying runoff also work for protection of water quality.