Conventional flooding paddy systems consume large amounts of water and results in water body pollution due to low water (WUE) and nitrogen use efficiencies (NUE). Therefore, rice production systems with water-saving and high resource use efficiencies need to be developed. A two-year field experiment was conducted in Fangxian County of Hubei Province in Central China. The experiment consisted of a conventional flooding paddy system (Paddy) and ground cover rice production system (GCRPS) with two different water management practices (i.e., GCRPSsat and GCRPS80%), factorially combined with three different N management practices (N1, no N fertilizer; N2, 150 kg urea N ha−1; and N3, 75 kg urea N ha−1 plus 75 kg N ha−1 as manure). In this study, we applied soil-crop system model (WHCNS, soil water heat carbon nitrogen simulator) coupled with simplified net mineralization model (LIXIM) to quantitatively evaluate water consumption, N fates, and rice growth under different N management practices for both Paddy and GCRPS. Results showed that the simulated soil water storage, soil mineral N content, leaf area index, dry matter, crop N uptake, and yield agreed well with the measured values. The Nash-Sutcliffe efficiency and index of agreement were greater than 0.51 and 0.86, respectively. Compared with Paddy, GCRPS significantly reduced the quantities of irrigation water (78.1%), nonproductive water consumption (evaporation, drainage, and runoff) (69.3%), and nitrate leaching (74.5%), and significantly enhanced yield (12.6%), WUE (42.8%), and NUE (20.0%). The WUE was ranked as follows: GCRPS80% > GCRPSsat > Paddy. In GCRPSs, GCRPS80% further decreased the nonproductive water consumption by 20.6% and did not reduce the yield compared with GCRPSsat. For different N management practices, no significant differences were found between the N2 and N3 treatments in terms of yields and NUEs. Meanwhile, the WUE of N3 (1.50 kg m-3) was significantly higher than that of N2 (1.41 kg m-3) in GCRPS. Hence, GCRPS80%_N3 was recommended as the best management practice for achieving high yield and high resource use efficiencies with the least environmental impact in the study region.