We conducted a study over four rice seasons to assess the effects of dairy manure application on water loss, nutrient leaching, and rice yield compared to chemical fertilization. Water input, soil water storage, water percolation, plant growth, and yield data were recorded under triplicate field lysimeters that received either chemical fertilizers or organic manure. The lysimeters received alternate wetting and drying irrigation (5-cm after 3 days (2018 Aman season), 6 days (2019 Boro and Aman seasons), and 9 days (2020 Boro season) of ponded water disappearance) in addition to rainfall (37.5, 33.1, 40.9, and 47.4 cm, respectively). Leachate and ponded water samples were analyzed for nitrogen (N) species (NH4+ - N and NO3- - N) and available phosphorus (P) content. Manure application increased soil water storage by 1.2-4.4 cm/m but did not affect percolation loss (44-64% of water input) in silt loam soil. The chemical fertilization had significantly higher leaching concentrations of nutrients (NO3- - N at 0.75-3.6 mg/L and P at 0.02-0.15 mg/L) in several leaching events in the last three seasons than the manure treatment (NO3- - N at 0.75-3.2 mg/L and P at 0-0.21 mg/L). Overall, the manure treatment reduced the leaching load of N and available P by 13% and 23.6%, respectively. The N and P concentrations in the topsoil were higher for the manure treatment. Manure application increased rice yield by 15% and water productivity by 0.07 kg/m(3) by augmenting soil water availability during the drying cycles of alternate wetting and drying processes. In addition, recycling manure in soil significantly reduced its environmental pollution compared to other inappropriate disposal methods. However, research needs remain important to adjust manure management options.