In order to improve paddy water and fertilizer management measures in Jianghan Plain, a field plot experiment with two irrigation regimes (conventional flooding irrigation, CF; shallow irrigation and deep storage, SIDS) and three nitrogen (N) managements (farmers' fertilization practice, FFP; 30% urea+70% controlled release compound fertilizer, 30%N+70%CRF; optimized and reduced nitrogen fertilizer application, OPT-N) was carried out to study the effects of water and fertilizer managements on losses of N and phosphorus (P), nutrition uptake of rice and nutrition accumulation of soil during different growth stages. The results were: (1) Compared with CF, SIDS reduced the irrigation quantity, total water use, runoff and leakage by 41.7%, 18.5%, 45.8% and 21.9%, respectively, but increased rainfall use efficiency by 16.2%. The amounts of total N (TN) from runoff and leakage in SIDS were 32.6%～35.9% and 22.8%～32.0% respectively lower than in CF. SIDS also decreased the amounts of total P (TP) from runoff and leakage by 36.4%～53.1% and 16.2%～33.3%, respectively. Meanwhile, the paddy runoff and leaching losses of TN and TP from re-greening to jointing and booting stages accounted for more than 70% of the whole growing season. (2) Compared with FFP, 30%N+70% CRF and OPT-N decreased runoff of TN by 19.7%～29.2% and 15.1%～25.2%, leaching losses of TN by 25.4%～51.7% and 20.9%～26.4%, leaching losses of TP by 18.4%～24.5% and 20.4%～31.6%, respectively, but no obvious difference was found in runoff of TP. (3) Considering the nutrients uptake of rice and nutrition accumulation in soil, compared with FFP, SIDS increased yield by 4.4%, but had no significant effects on N and P accumulation in soil (0-40 cm depth). Compared with FFP, 30%N+70% and OPT-N improved 5.6% and 0.4% yields respectively, and also giving the high and stable available N and available P in soil (0—20 cm depth). In generally, the combination of SIDS and 30%N+70% CRF could be effective in saving water, reducing N and P losses, promoting rice yields and improving soil fertility.