China is a large country with a long agricultural history. Rice has been cultivated in China for more than 7000 years, and ducks have been domesticated there for about 3000 years. To improve and strengthen ecological functions of the rice–duck farming system, other organisms are often artificially introduced into the paddy field together. The biological factors usually include rice, ducks, weeds, rice pests and their natural enemies, rice diseases, aquatic plants and animals, soil microbes, and soil animals. The vertical structure of the farming system can be divided into five layers from upper to lower: the upper rice canopy layer, middle canopy layer, lower canopy layer, water layer, and soil layer. The weed biomass in the rice–duck system with grazing and disturbance was significantly lower than that in the other treatments at both sampling stages. Generally, duck activities can effectively reduce incidences of rice diseases, either directly or indirectly, and usually via the following pathways.