Sewage effluents are increasingly used for farmland irrigation worldwide. This practice makes N losses via gaseous forms and leaching process more complex. Twelve repacked lysimeters with 90 cm height and 25 cm inner diameter were used for comprehensively determining ammonia (NH3) and nitrous oxide (N2O) emissions and N leaching losses in a rice-wheat cropping system irrigated with N-rich wastewater from a livestock pond. There were four irrigation treatments with three replications: wastewater with high N concentration (HW), wastewater with medium N concentration (MW, one-half dilution of wastewater of HW), wastewater with low N concentration (LW, one-fourth dilution of wastewater of HW), and ultrapure water control (CK). All treatments received equal amounts of total N (225 kg N ha−1 in the rice season and 150 kg N ha−1 in the wheat season) by balancing with commercial N fertilizer. The wastewater was proven to be as effective as commercial N fertilizer to achieve the optimum crop yields when applied in an appropriate amount. The NH3 emission, N leaching, and N2O emission losses accounted for 16.2 to 19.8%, 4.6 to 6.4%, and 0.26 to 0.35% of the total N applied in the rice season, respectively, whereas they were 2.7 to 3.3%, 2.2 to 2.8%, and 0.77 to 1.0% in the wheat season. Irrigating with wastewater did not change the NH3 emission flux pattern after N fertilizer (urea) was applied, but it boosted the NH3 emission flux to a certain extent in the rice season, especially for the MW treatment, which was mainly attributed to the high ammonium content and pH of the flood surface water resulting from a combined effect of wastewater and urea-N application. In addition, N-rich wastewater irrigation did not significantly increase N2O emission and N leaching when the total N inputs and the amount of irrigation were the same.