Water rights trading is an important policy instrument to resolve the problem of water scarcity. However, the third-party effect of water rights trading is a serious challenge to the efficiency and fairness of the market. From the perspective of implicit property rights, this paper explores the formation mechanism of the third-party effects of agricultural water rights trading and the impact of the characteristics of different agricultural water rights trading types on the formation of third-party effects. This paper finds that, due to the significant spatial characteristics of agricultural water rights, changes in the spatial characteristics of water rights and the technical characteristics of water use in the process of water rights trading result in third-party effects, such as return flow effects, water quantity effects, water quality effects, and water cost effects, which have an impact on the attributes of water resources in public water areas and thereby affecting the attributes of water rights and the implicit property rights. Consequently, the water rights of other water users outside of the water rights trading will be influenced. Water rights trading between industries leads to significant third-party effects because the trading not only changes the industrial, locational, and technological characteristics of water use but also has the characteristics of large-scale and long-duration trading. In contrast, water rights trading in agriculture, being smaller in scale and shorter in duration, yields weaker third-party effects, with specific impacts depending on trading characteristics. Clarifying the implicit property rights in water rights and implementing tailored regulation measures based on the trading characteristics of different water rights trading types are key to governing the third-party effects of agricultural water rights trading.