(1) Background: Arid conditions occur due to climate abnormality in the different biogeography regions of the world. The aim of this research is to investigate the stoichiometry of manure and moisture regimes on soil properties, microbial biomass C:N:P turnover, and the grain yield of mustard crops under stress in arid conditions; (2) Methods: The field experiment was carried out for 2 years at the farms of the agriculture college of SKN, Jobner (SKRAU Bikaner, Rajasthan). The effects of organic manure, moisture regimes, and saline water treatment on soil properties, such as the soil microbial biomass build-up, loss, turnover, and recycling of carbon (Cmic), nitrogen (Nmic), and phosphorus (Pmic) in the mustard crop were investigated. The twenty-seven treatments studied are described as follows: organic manures (control, FYM @ 10 t ha−1 and vermicompost @ 5 t ha−1), moisture regimes (0.4, 0.6, and 0.8 IW/CPE ratio), and saline irrigation water (control, 6, 12 dSm−1); (3) Results: Our findings indicate that vermicompost @ 5 t ha−1 significantly increases moisture retention and the available water in soil at 33 kPa and 1500 kPa. The microbial biomass build-up of Cmic increases by 43.13% over the control and 14.36% over the FYM. Similarly, the soil microbial biomass of Nmic, and Pmic also increase considerably. The SHC of the soil is enhanced by the application of farmyard fertilizer and vermicompost. The BD and pH decrease significantly, while the SHC, OC, CEC, and ECe of the soil increase significantly. The build-up, losses, and fluxes of the soil microbial biomass of Cmic, Nmic, and Pmic increase significantly, and the turnover rate decreases under vermicompost @ 5 t ha−1. A significant increase in grain yield was observed. Irrigation with a 0.8 IW/CPE moisture regime significantly decreases the pH of the SHC; (4) Conclusions: We hypothesized the interactive outcomes of the moisture regime and found that organic manure significantly influenced grain and stover yield. The treatments of quality irrigation water and the addition of organic manure are efficient enough to improve soil properties, water holding capacity, and soil microbial biomass C:N:P in stress climatic conditions.