Soil microbial communities are critically important for the transformation of nitrogen in agricultural farmlands. The effects of muddy water irrigation with different sediment particle sizes and sediment concentrations on microbial communities in the Yellow River Basin of China have not yet been studied. The 16 S rRNA profiles of bacterial communities in paddy soils were characterized using an orthogonal experiment with four moisture treatments (60%, 80%, and 100% water-filled pore space (WFPS), and drowned), four sediment particle sizes (d₅₀ = 0.017, 0.038, 0.046, and 0.069 mm), and four sediment concentrations (0%, 1%, 5%, and 10%). Proteobacteria, Bacteroidetes, Gemmatimonadetes, Acidobacteria, Chlorobi, and Nitrospirae were the most abundant phyla, and Azospirillum, Limnobacter, Methylophaga, Ramlibacter, Mesorhizobium, Anaeromyxobacter, Geobacter, Candidatus_Solibacter, Gallionella, and Rubrivivax were the most abundant nitrogen-related genera across all treatments. Soil bulk density (SBD) was significantly correlated with Azospirillum, Limnobacter, Methylophaga, Geobacter, and Gallionella. Alpha diversity was highest in the treatment with 100% WFPS, 1% sediment concentration, and 0.069 mm particle size. pH, NH₄⁺, and NO₃^- were most closely related to the relative abundance of nitrogen-related genera according to correlation analysis. Redundancy analysis (RDA) showed that SBD was the most important factor affecting soil microorganisms; however, NH₄⁺ and NO₃^- also had substantial effects on soil microorganisms. Structural equation modeling revealed that SBD and pH were the most important factors affecting nitrogen transformation and the microbial community; however, NO₃^-, NH₄⁺, and the nitrification rate also had significant effects. Overall, the results indicate that muddy water irrigation can be used to enhance the diversity of the soil microbial community. The findings will also aid future research examining the effects of moisture and sediment variables on soil microbial communities in the Yellow River Basin.