Water stress and nutrient supply are two of the most ubiquitous global changes that surely drive substantial variations not only in agricultural productivity but also extend to alert soil living organisms. The present study aims to understand the intrinsic changes in the composition of soil populations and their functions due to the interaction between long-term fertilization and rainfall fluctuations, seeing whether fertilization history would render the soil microbial communities and their activities more resistant to water stress or not. The experiment was established in 1988 on a typical meadow soil (Vertisols) as a rainfed maize monoculture receiving six elevated rates of NPK annually. The 30-year average annual precipitation of the growing season in this region is 345.1 mm. However, in 2010 rainfall was 106.1% greater than the average, while in 2011 it was 26.5% lower. The results show that long-term NPK fertilization has made the soil microbes more tolerant to changes in soil moisture content resulting from rainfall fluctuations. Soil microbes and their activities, however, did not follow a dose-response relationship of NPK as soil moisture content was the main driving factor. Numbers of total fungi, cellulose decomposing bacteria, and nitrifying bacteria increased as rainfall in 2010 increased. Moreover, microbial biomass carbon in 2010 was almost 2-fold higher than in 2009. Soil respiration in 2010 was 11 and 35% higher than in 2009 and 2011, respectively. Otherwise, high rainfall in 2010 significantly diminished soil NO3- content and nitrification rate. Soil enzyme activity showed a higher response to soil moisture than the rate of NPK. The highest activity of phosphatase, dehydrogenase, and saccharase was measured in the driest year (2011), while urease displayed its highest activity in 2010. High rates of NPK significantly reduced soil dehydrogenase activity. These results illustrate how important it is for fertilizer programs to be flexible to match expected climate change in order to improve productivity and reduce environmental pollution.