Based on the analysis of soil samples in four different hydrologic conditions of the Lijiang Riparian Zone, i.e., gravel zone, grass zone, shrub-grass zone, and tree zone, this study explored the variation characteristics and relationships among soil nutrients, microbe quantity, and microbial biomass. The results showed significant differences in soil nutrients and microbes among various hydrologic conditions. As the submersion duration decreased, the value of soil water content (SWC), pH, available nitrogen (AN), available phosphorus (AP), and available potassium (AK) increased and then decreased, the highest value usually appeared in the shrub-grass zone, whereas the lowest was in the gravel zone. The total amount of soil microbes, bacteria, actinomycetes, and microbial biomass carbon, nitrogen, and phosphorus (MBC, MBN, MBP) also exhibited an increasing-decreasing trend, and reached a maximum in the shrub-grass zone and a minimum in the gravel zone. Simple correlation analysis showed that various indexes of microorganisms were closely related to AN, AP, and AK and had a loose relationship with total nitrogen (TN), total phosphorus (TP), and total potassium (TK). Redundancy analysis revealed that AN, AP, and SWC were important factors affecting the total amount of microbe, bacteria, and microbial biomass C, N, and P, and soil organic matter (SOM) and TN were important factors affecting the amount of actinomycetes. The above results suggested that appropriate hydrologic disturbance was beneficial to the soil nutrient accumulation, and also had a positive impact on the soil microbes and their biomass. The SOM and available nutrients (AN, AP) were closed to soil microbes, and their contents greatly affected the quantity and activity of soil microbes. In the research process of ecological protection and assessment of the Lijiang riparian zone, the variation characteristics and relationship between soil microbes and nutrients under different hydrological conditions must be considered.