With the rapid expansion of global agriculture, phosphorus pollution from nonpoint sources has emerged as a major constraint to water quality improvement. Among the methods used to control nonpoint-source pollution, small water bodies such as ditches and ponds have received increasing attention due to their widespread distribution and low cost. However, most previous studies have focused on specific regions, and the key factors regulating phosphorus retention and their generalizable patterns remain unclear. Additionally, research on the synthesis of global water-body nutrient retention is largely limited to studies from North America and Europe. Here, we compiled a phosphorus retention dataset for small water bodies across China that incorporates research published in Chinese. Using multiple statistical analyses to assess the hydrological processes and external influencing factors on phosphorus removal rate and efficiency, our results show that the median total phosphorus removal rate in ditches and ponds across China was 33.7%. Among all hydrological and external influencing factors, hydraulic retention time (HRT) served as a pivotal parameter in the modulation of phosphorus removal efficiency. Extending HRT is an effective method to enhance phosphorus retention in water bodies, although it also demonstrates diminishing marginal returns. By regulating the HRT of small water bodies, a win–win situation with both pollutant reduction and agricultural production may be achieved, thereby enhancing the resilience of agricultural ecosystems to climate change. This study provides a scientific basis and technical support for achieving the dual goals of sustainable agricultural development and environmental improvement in developing countries—particularly in rice-producing regions.