A field experiment was conducted during rainy (kharif) season of 2018–19 and winter (rabi) season of 2019–20 at the Water Management Research Farm of CSK Himachal Pradesh Agricultural University, Palampur, Kangra, Himachal Pradesh to study the effect of moisture and nutrient management practices on different soil microbial entities and crop yields in rice (Oryza sativa L.)–wheat (Triticum aestivum L.) system. Experiment was laid out in a split-plot design with 3 replications. Treatments comprised of 3 irrigation levels, viz. Recommended critical stages regimes; Irrigation at 0.8 CPE (cumulative pan evaporation) (rice) and 0.6 CPE (wheat); Irrigation at 1.0 CPE (rice) and 1.0 CPE (wheat) assigned to main-plots and 4 nutrient management practices, viz. Inorganic; Organic; Natural farming; and Integrated management allotted to sub-plots. Irrigation at critical stages resulted in significantly higher rice yield, bacterial, azotobacter, phosphate solubilizing bacteria (PSB), actinomycetes population. However, fungi population increased under higher moisture regimes. In case of wheat crop, irrigation at 1.0 CPE resulted in a significantly higher yield (7.5% higher over irrigation at critical stages) in both the years of study. Organic and integrated nutrient management practices being statistically at par with each other recorded significantly higher microbial population. A significantly higher fungi population was, however, recorded with natural farming. The highest crop yields were obtained with integrated nutrient management (3.4 t/ha rice and 3.6 t/ha wheat in second year). The best combination for rice was irrigation at critical stages along with integrated nutrient management. Whereas, for wheat irrigation at 1.0 CPE with same nutrient management proved to be the best. Hence it is recommended to follow integrated nutrient management and irrigation at critical stages in rice and at 1.0 CPE in wheat for higher productivity as well as for improved biological properties of soil.