This study aims to investigate the effects of muddy water irrigation and bio-organic fertilizers on soil water infiltration, evaporation, and leaching in the cultivated layer of Xi'an Province, China. An indoor one-dimensional soil column infiltration device was also utilized in the experiment. Four levels of muddy water sediment concentration (0, 4%, 8%, 12%, quality fraction, sediment from the muddy infiltration water was collected from the bottom of the Jinghui Canal irrigation area in the Yellow River basin, China) and four levels of bio-organic fertilizers (0, 2 250, 4 500, 6 750 kg/hm², bio-organic fertilizer from Yuanlong Biotechnology Co., Ltd., Puyang, China.) were set in a total of 16 treatments, where each repeated three times. The experimental indicators were measured, such as the cumulative infiltration, wetting front transport distance, soil water evaporation, soil moisture content, electrical conductivity, organic matter content, and leaching solution loss. The models were about: 1) the relationship between the infiltration time, sediment concentration in muddy water, fertilization amount, and wetting front distance; 2) the relationship between infiltration time, sediment concentration in muddy water, fertilization amount and infiltration rate; 3) The cumulative evaporation and evaporation time were fitted using Black and Rose evaporation models. The results showed that the sediment concentration of muddy water and bio-organic fertilizer posed the significant effects on the wetting front distance, cumulative infiltration amount, and infiltration rate. The higher the muddy water sediment concentration and bio-organic fertilizer level were, the smaller the wetting front distance and cumulative infiltration amount within the same infiltration time were. The muddy water infiltration increased the infiltration time by 9.88%-70.37%, whereas, the cumulative infiltration was reduced by 13.17%-34.13%, compared with the clean water infiltration. The bio-organic fertilizer was applied to increased the infiltration time by 8.96%-51.09%, while the cumulative infiltration amount was reduced by 0.91%-20.69%, compared with no fertilization. The wetting front distance and infiltration time were conformed to the power function relationship, where the coefficient of determination (R²) was more than 0.9. The Kostiakov infiltration model was used to fit the soil water infiltration characteristics and parameters under muddy water irrigation and fertilization conditions (R²>0.9). The infiltration coefficient K gradually decreased, as the muddy water sediment concentration and fertilization level gradually increased, while the infiltration index ɑ enlarged gradually. Muddy water irrigation and bio-organic fertilizer were effectively reduced the soil water evaporation, where the muddy water infiltration was reduced cumulative evaporation by 10.44%-26.24%, compared with clean water infiltration. The bio-organic fertilizer was reduced the accumulated evaporation by 4.76%-15.83%, compared with no fertilization. The cumulative evaporation amount and evaporation time under muddy water irrigation and bio-organic fertilizers conditions were consistent with the Black and Rose evaporation models (R²>0.9), and the SRMSE value of the Black evaporation model was lower than that of the Rose model, indicating that the accuracy of the Black evaporation model was higher than that of the Rose evaporation model. After evaporation, the soil moisture content, electrical conductivity, and organic matter content increased with the increase of soil depth. The pH value in the leaching solution increased with the increase of leaching time, while the electrical conductivity and total dissolved solids decreased with the increase of in leaching time. The muddy water irrigation increased the conductivity, organic matter content in the soil and total dissolved solids in the leaching solution, while reducing soil moisture content, pH, and leaching solution volume, compared with the clean water infiltration. Furthermore, the bio-organic fertilizer was applied to reduce the leaching solution volume, and conductivity, and total dissolved solids in the leaching solution, whereas there was an increase in the organic matter content and conductivity in the soil, compared with no fertilization. Therefore, the better performance was achieved in the muddy water irrigation, bio-organic fertilizer and soil infiltration capacity, and water and fertilizer conservation capacity. The finding can provide the scientific reference for the efficient utilization of muddy water and rational application of bio-organic fertilizer in the arid and semi-arid areas of the Yellow River Basin.