This study investigates the impact of water levels and soil texture on the migration and transformation of nitrate (NO3−-N) and ammonium (NH4+-N) within a soil column. The concentrations of NO3−-N gradually decreased from an initial concentration of 34.19 ± 0.86 mg/L to 14.33 ± 0.77 mg/L on day 70, exhibiting fluctuations and migration influenced by water levels and soil texture. Higher water levels were associated with decreased NO3−-N concentrations, while lower water levels resulted in increased concentrations. The retention and absorption capacity for NO3−-N were highest in fine sand soil, followed by medium sand and coarse sand, highlighting the significance of soil texture in nitrate movement and retention. The analysis of variance (ANOVA) confirmed statistically significant variations in pH, dissolve oxygen and oxidation–reduction potential across the soil columns (p < 0.05). Fluctuating water levels influenced the migration and transformation of NO3−-N, with distinct patterns observed in different soil textures. Water level fluctuations also impacted the migration and transformation of NH4+-N, with higher water levels associated with increased concentrations and lower water levels resulting in decreased concentrations. Among the soil types considered, medium sand exhibited the highest absorption capacity for NH4+-N. These findings underscore the significant roles of water levels, soil texture, and soil type in the migration, transformation, and absorption of nitrogen compounds within soil columns. The results contribute to a better understanding of nitrogen dynamics under varying water levels and environmental conditions, providing valuable insights into the patterns of nitrogen migration and transformation in small-scale soil column experiments.