Field experiments were carried out to study the effects of applying an amino acid fertilizer on enzyme activities and available nutrients in rhizosphere and bulk soils of two varieties of different disease-resistance cotton at Shihezi city in Xinjiang in 2006 with open flooding irrigation and in 2007 with film-covered trickle irrigation. Soil samples were collected at the bolling stage. The results showed that the activities of catalase, alkaline phosphatase, urease and cellulase, urease and cellulase were significantly higher in rhizosphere soils than those in bulk soils. The activities of catalase, alkaline phosphatase, urease and cellulase except catalase in rhizosphere soils of variety Xinluzao-8 were lower than those of variety Xinluzao-12. The contents of available nitrogen increased while available phosphorus decreased in rhizosphere soils in comparison with bulk soils. When compared to the open flooding irrigation, the film-covered trickle irrigation increased the activities of catalase, alkaline phosphatase, urease, and soil pH in both rhizosphere and bulk soils, the contents of available N and P in bulk soils and available K in rhizosphere soils, but decreased the activities of catalase and cellulose, and the contents of available N and P in rhizosphere soils as well as available K in bulk soils. Applying amino acid fertilizer can increase the activities of soil enzymes and the contents of available nutrients either in rhizosphere or bulk soils but decrease soil pH in rhizosphere soil when high dose of the fertilizer is used. In conclusion, agronomical practices such as fertilizer use and irrigation as well as crop variety can affect the soil biological and chemical properties, of which effects on crop growth and health need to be understood.