Irrigating aquaculture wastewater in appropriate irrigation and drainage modes in paddy fields could reduce water and fertilizer loss. However, the precise mechanisms involved in the degradation and movement of nitrogen in various water and fertilizer modes are still not fully understood. This study involves conducting a controlled experiment using barrels to examine the effects of various water quality, irrigation and drainage methods, and fertilization levels. The aim is to analyze the patterns of nitrogen degradation, loss, migration, and absorption in surface water, underground drainage, and soil leakage at different depths. The results showed the following: (1) The paddy field has a significant purification effect on aquaculture wastewater after one day of irrigation, reached at 78.55–96.06%. (2) Aquaculture wastewater irrigation increased nitrogen concentration in the plough layer, which helps rice roots absorb nitrogen and boosts plant TN. (3) In special dry years, underground seepage is the predominant method of nitrogen loss, and underground drainage nitrogen concentration peaks 2–6 days after fertilization. (4) Under aquaculture wastewater irrigation, the TN loss load of II decreased by 27.65–42.45% than FSI. Compared with IA-80, the TN degradation rate of IA in surface water increased by 18.51%, TN loss load decreased by 5.48%, TN absorption rate significantly increased by 14.61%, and yield increased by 31.14% significantly. IA is recommended in special dry years, which can improve the TN absorption rate and ensure high yield while significantly reducing the loss load of nitrogen. The findings can provide a basis for the purification of aquaculture wastewater through paddy field ecosystems in response to fertilizer supply levels.