Human-induced nitrogen-phosphorus (N, P) imbalance in terrestrial ecosystems can lead to disproportionate N and P loading to aquatic ecosystems, subsequently shifting the elemental ratio in estuaries and coastal oceans and impacting both the structure and functioning of aquatic ecosystems. The N:P ratio of nutrient loading to the Gulf of Mexico from the Mississippi River Basin increased before the late 1980s driven by the enhanced usage of N fertilizer over P fertilizer, whereafter the N:P loading ratio started to decrease although the N:P ratio of fertilizer application did not exhibit a similar trend. Here, we hypothesize that different release rates of soil legacy nutrients might contribute to the decreasing N:P loading ratio. Our study used a data-model integration framework to evaluate N and P dynamics and the potential for long-term accumulation or release of internal soil nutrient legacy stores to alter the ratio of N and P transported down the rivers. We show that the longer residence time of P in terrestrial ecosystems results in a much slower release of P to coastal oceans than N. If contemporary nutrient sources were reduced or suspended, P loading sustained by soil legacy P would decrease much slower than that of N, causing a decrease in the N and P loading ratio. The longer residence time of P in terrestrial ecosystems and the increasingly important role of soil legacy nutrients as a loading source may explain the decreasing N:P loading ratio in the Mississippi River Basin. Our study underscores a promising prospect for N loading control and the urgency to integrate soil P legacy into sustainable nutrient management strategies for aquatic ecosystem health and water security.