<p>This study combined with field sampling monitoring and the Hydrus-1D model to study the migration and transformation of organic acids discharged from high-elevation shrimp ponds into the soil of estuarine mangrove wetlands, and numerical simulation. The results showed that the organic acids discharged from shrimp ponds were enriched and settled in the soil of mangrove wetlands. Tidal creek and mangrove damaged areas had the highest organic acid content along the way, which decreased after entering the core protected area, with the spatial variation of its content manifested as a continuous decrease in the 0–50 cm sediment soil with increasing depth. The total organic acid concentration in the tidal creek of the Yanfeng area was close to the organic acid toxicity threshold of mangrove plants, indicating that the area was greatly affected by shrimp farming activities. The simulation results using Hydrus-1D are in good agreement with the field detection results.</p>