Use of saline water in irrigated agriculture has become an important means for alleviating water scarcity in arid and semi-arid regions. The objective of this field experiment was to evaluate the effects of irrigation water salinity and N fertilization on soil physicochemical and biological properties related to nitrification and denitrification. A 3×2 factorial design was used with three levels of irrigation water salinity (0.35, 4.61 and 8.04 dS m^–1) and two N rates (0 and 360 kg N ha–¹). The results indicated that irrigation water salinity and N fertilization had significant effects on many soil physicochemical properties including water content, salinity, pH, NH₄-N concentration, and NO₃-N concentration. The abundance (i.e., gene copy number) of ammonia-oxidizing archaea (AOA) was greater than that of ammonia-oxidizing bacteria (AOB) in all treatments. Irrigation water salinity had no significant effect on the abundance of AOA or AOB in unfertilized plots. However, saline irrigation water (i.e., the 4.61 and 8.04 dS m^–1 treatments) reduced AOA abundance, AOB abundance and potential nitrification rate in N fertilized plots. Regardless of N application rate, saline irrigation water increased urease activity but reduced the activities of both nitrate reductase and nitrite reductase. Irrigation with saline irrigation water significantly reduced cotton biomass, N uptake and yield. Nitrogen application exacerbated the negative effect of saline water. These results suggest that brackish water and saline water irrigation could significantly reduce both the abundance of ammonia oxidizers and potential nitrification rates. The AOA may play a more important role than AOB in nitrification in desert soil.