<p>To address the rising contradiction between food security and eco-environment pollution originated from massive fertilizers are input into paddy fields for achieving the highest yield to meet the continuously increasing of global population. A test has been performed in a double-cropping rice in Jiangshan city in China. This work investigated the nutrient concentrations of paddy ponded water and evaluated potential losses risks over a double-cropping rice with 3 fertilization frequents (FF: 1, 2, and 3) and 2 fertilization depths (FD: surface broadcast (SB) and deep application (DA)). Compared to one-time fertilization, 2–3 FF significantly decreased daily mean concentration in ponded water by 13.7–28.2% for TN, 22.1–25.0% for NH₄⁺-N, 9.8–14.6% for TP, and 7.7–15.4% for WSP, respectively. Compared with SB of fertilizers, there were a decrease of 36.9% for TN, 30.9% for NH₄⁺-N, 21.4% for TP, 28.6% for WSP, 29.9% for TK, and 29.6% for WSK by DA, respectively. Furthermore, the interaction between FF and FD displayed the effect of FF on N/P concentration only in the case of surface broadcasting. These results indicated both split- and deep-application of fertilizer can effective lowers nutrient concentrations of ponded water and further potential loss risk. This highlights the need for reasonable fertilization ways in paddy fields to maintain sustainable rice production, and fertilization strategies with 2-splits combining with deep application of basic fertilizer can be recommend as priority options.</p> Graphical Abstract <p></p>