We studied controls on nitrification in an undisturbed water-limited ecosystem by inhibiting autotrophic nitrifying bacteria in soils with varying levels of vegetative cover. The activity of nitrifying bacteria was disrupted using nitrapyrin, 2-chloro-6-(trichloromethyl)-pyridine, under field conditions in three microenvironments (underneath shrubs, next to grasses and in bare soil). Ammonia-oxidising bacteria were detected by PCR analysis of DNA in soils. The inhibition of nitrification changed the concentrations of NO3− and NH4+ in the soil, while the microenvironment was most important in determining the response of bacteria to the inhibitor. Nitrapyrin application resulted in a significant (p<0.05) reduction in soil NO3− concentration (39%) and a significant increase (p<0.001) in soil NH4+ concentration (41%). Untreated bare-soil microenvironments had the lowest concentrations of NH4+ (1.57 μg/g of dry soil) and NO3− (0.49 μg/g of dry soil) when compared to the other microenvironments, and showed the highest impacts of nitrification inhibition. For example, NH4+ concentrations increased 288% and NO3− concentrations decreased 60% in inhibited bare-soil microenvironments. In contrast, untreated microenvironments underneath shrubs had the highest levels of NH4+ (10.01 μg/g of dry soil) and NO3− (0.69 μg/g of dry soil), but showed no significant effects of inhibition of nitrification on soil nitrogen concentrations.