Excessive fertilizer or unseasonable fertilization ways are common in rice-cultivated regions over world, and a consequence is an environmental adverse impact resulting from substantial nutrient losses. In order to evaluate the influence of fertilization ways on nutrient losses in flooding paddy field, this work investigated the dynamic of nutrient concentrations via a short-term experiment containing single- and split-application fertilizer during main fertilization period, in the Jiangshan city, Zhejiang, China. The ponded water nutrient concentrations from fertilization plots ranged widely over the experiment: 2.8–80.9 mg L⁻¹ for NH₄⁺-N, 0.2–3.7 mg L⁻¹ for NO₃⁻-N, 1.2–215.0 mg L⁻¹ for TN, 0.02–0.6 mg L⁻¹ for TP, and 0.5 to 48.8 mg L⁻¹ for TK, respectively. Applying mineral fertilizer increased immediately nutrient concentrations in ponded water and followed by a slow drop to a stead levels. The results showed a high-risk period of losses was within 3–5 days for N and 8–11 days for K following fertilization, respectively, if runoff occurred by rainstorm or drainage depending on fertilization ways. The losses risk of ponded water P after basal fertilization was negligible, but within 5 days after first topdressing was a potential pollution risk period. Compared to split fertilization, single fertilization can reduce losses risk via runoff by 66.3–67.5% for N and by 36.9–46.8% for K, respectively. However, in addition to rice yield reduction, the single application as basal fertilizer may enhance losses by NH₃ volatilization, which led to a high risk of air pollution, and decrease the pH of ponded water and further soil acidification as well. Hence, the results suggested that the fertilizer split-application containing panicle fertilizer can consider as an ecological fertilization way and is suitable for rice main production region which benefit for both economic and environment despite a little increase of labor costs.