This study was conducted to evaluate the effect of a mole drainage under irrigation management practices in paddy rice cultivation on the chemical properties of paddy soils and rice yield. The experiment was implemented as a split-plot arrangement within a randomized complete block design with three replications during the 2022–2023 at the research farm of the University of Guilan, Rasht, Iran. Treatments included a control without drainage (D0), traditional mole drainage (D1; ), and gravel-filled mole drainage (D2), combined with continuous flooding (I1) and alternate wetting and drying (I2) irrigation regimes. Mid and end-season drainage was applied at the tillering stage, and harvest time. To assess temporal changes in soil chemical properties, soil samples at four growth stages and from two soil depths. Soil pH, electrical conductivity, nitrate and ammonium concentrations, and sodium, calcium, and magnesium contents were measured. After harvest, rice grain yield was determined. Statistical analysis of surface and subsurface layers showed that the effect of mole drainage (except for nitrate and pH), the effect of sampling time (except for pH), and the interaction between mole drainage and sampling time were significant at the 1% probability level for all measured soil chemical parameters. Comparison of soil conditions before and after mid-season drainage indicated that drainage reduced ammonium concentrations by 43% and 26% and increased nitrate concentrations by 47% and 46% in the surface and subsurface layers, respectively. Drainage also decreased soil electrical conductivity by 27% in the surface layer but increased it by 12% in the deeper layer. The highest grain yield (5187.24 kg ha⁻¹) was obtained under gravel-filled mole drainage , which represented increases of 2.8% and 10.5% compared with traditional mole drainage and the control, respectively. The application of mole drainage, particularly when combined with gravel, altered soil chemical properties and led to increased rice yield.