Palladium (Pd) is widely used in automotive catalytic converters to reduce toxic gas emissions. The input of Pd in the rainfall-runoff is an important contributing factor to the accumulation of Pd in receiving water bodies. In this study, the Meishe River in Haikou, Hainan Province, China, was used as the research area, and palladium (Pd) was selected as the target pollutant. This study explored the response of Pd in the receiving water body to rainfall-runoff and to analyze the influencing factors. The results showed that the dissolved Pd concentration in the receiving water body had a corresponding relationship with that in rainfall-runoff. The response of suspended Pd in the receiving water body to rainfall-runoff was closely related to the location of the drainage outlet. Compared with that of suspended Pd, the response of dissolved Pd in the receiving water body to that in the rainfall-runoff was more obvious. Seven meters downstream from the outfall was the most sensitive response distance of dissolved Pd in receiving water bodies to rainfall-runoff, and the response time was approximately 0–10 min. The suspended Pd at 3 m downstream from the outfall also had a certain response to the rainfall-runoff, and the response time was approximately 15–25 min. The response time of the suspended Pd in the receiving water body depended largely on the first flush ability of the runoff. There was a moderately positive correlation between the dissolved Pd and Cl− in the receiving water body (r = 0.687; p < 0.05). The effects of pH, Eh, and total suspended solids (TSS) on suspended Pd were reduced in the response process of the receiving water body. The synergistic effect of multiple factors increased the uncertainty of the Pd response.