The aim of this study was to assess the influence of season, farm management (organic, biodynamic, integrated, and conventional), and soil chemical, physical, and biological properties on gross nitrogen (N) fluxes and bacterial community structure in the semi-arid region of Western Australia. Moisture availability was the dominant factor mediating microbial activity and carbon (C) and N cycling under this climate. In general, microbial biomass N, dissolved organic N, and potentially mineralisable N were greater in organic and biodynamic than integrated and conventional soil. Our results indicate that greater silt and clay content in organic and biodynamic soil may also partly explain these differences in soil N pools, rather than management alone. Although plant-available N (NH₄⁺ + NO₃^–) was greater in conventional soil, this was largely the result of higher NO₃^– production. Multiple linear modelling indicated that soil temperature, moisture, soil textural classes, pH, electrical conductivity (EC), and C and N pools were important in predicting gross N fluxes. Redundancy analysis revealed that bacterial community structure, assessed by denaturing gradient gel electrophoresis of 16S rDNA, was correlated with C and N pools and fluxes, confirming links between bacterial structure and function. Bacterial community structure was also correlated with soil textural classes and soil temperature but not soil moisture. These results indicate that across this semi-arid landscape, soil bacterial communities are relatively resistant to water stress.