Estuarine and coastal ecosystems are critical biogeochemical interfaces regulating land-sea nutrient exchange, yet the coupled mechanisms of nitrogen (N) and phosphorus (P) cross-interface transport and their ecological feedbacks under multi-timescale disturbances remain poorly quantified. Most existing studies focus on steady-state background conditions, lacking systematic discrimination of short-term hydrological perturbations and long-term cumulative ecological recovery processes. This study integrates high-frequency in-situ observation and a coupled deep learning model to clarify the N-P dynamic transport fluxes across estuary-coast interfaces. We reveal that typhoon-induced hydrology variation dominates nutrient enrichment and long-distance seaward migration, while extreme hydrological events such as typhoon-induced floods trigger abrupt short-term flux perturbations distinct from base-flow conditions. Furthermore, this research quantifies the lagged ecological responses including nutrient ratio imbalance, chlorophyll-a variation and phytoplankton community succession, and establishes a timescale-dependent recovery framework for eutrophic systems. The results identify critical threshold values of nutrient flux reversal that determine ecosystem recovery resilience, correcting the linear response bias of traditional nutrient biogeochemical models. This work provides a multi-scale mechanistic understanding of land-sea nutrient cycling and offers targeted scientific support for integrated watershed-coastal eutrophication mitigation and ecological restoration under changing environments.