Abstract: Grey water footprint (GWF) can be used as an indicator to quantitatively evaluate the impact of agricultural production process on water environment. Traditional methods for calculating GWF of crop production are usually based on rough estimation, which cannot accurately quantify the difference between GWFs caused by fertilizer types. In this study, field experiments were conducted to observe the migration process of water and fertilizer in paddy field under conventional fertilization (CF), biochar-based fertilizer (BF) and organic fertilizer partially replacing chemical fertilizer (OF) treatments. This study aimed to identify the most critical pollutants for each runoff event and to explore the changes in the GWF under different fertilization types. The results showed that: (1) Compared with CF treatment the BF treatment and OF treatment both reduced the pollutant losses of total nitrogen, nitrate nitrogen, ammonium nitrogen and total phosphorus, and increased rice yields by 3.48% and 6.81%, respectively. (2) In all runoff events produced during the study period, the occurring frequency of total nitrogen as the key pollutant was the highest, while total phosphorus was also critical pollutants under certain circumstances, implying that the key pollutant determining the amount of grey water was variant. (3) The impacts of fertilizer typeson the GWF of rice production were in the order of: CF (622.85 m³/t) > BF (367.68 m³/t) > OF (318.18 m³/t). OF reduced the grey water footprint of rice production and increased the rice yield, which help achieve the goal of pollution reduction and yield increase. The method for calculating GWF of crop production based on field measurements can accurately quantify the influence of different fertilizer types on grey water footprint.