The APSIM–Oryza model has been used worldwide to evaluate the impact of diverse management practices on the growth of rice (Oryza sativa L.). Despite its importance, the crop productivity (kg ha−1) and water productivity (kg ha−1 mm−1) of rice under moisture-limited (i.e. rainfed or rainfed with supplementary alternate wetting-and-drying (AWD) irrigation) farmer-field conditions in tropical South-Asia has received little attention in modelling exercises. Benefits of aligning crop establishment with the onset of rainfall to reduce dependency on supplementary irrigation and improve crop and water productivities have not yet been quantified in Sri Lanka. Therefore, we parameterised and evaluated the APSIM–Oryza model for two widely grown Sri Lankan short- and medium-duration rice varieties. The model estimated the grain yield of rice under moisture-limited farmer-field conditions with a strong fit (n = 24, R2 > 0.97, RMSE = 484 kg ha−1), across cultivation year, season, time of establishment (i.e. with rainfall onset or date-specific planting), variety and/or water management practice (i.e. totally rainfed or rainfed with supplementary irrigation). A climatic analysis indicated that the farmers regularly establish rice crops 2–4 weeks after the rainfall onset. This is a consequence of the current practice of setting the date for crop establishment at pre-season cultivation meetings without a scientifically-validated rainfall forecast. The same analysis revealed that an early onset to the rainy season resulted in longer seasons with more rain than late onset. When the onset of rainfall is delayed, crop modelling scenarios using the validated APSIM model showed an increased dependence on supplementary irrigation for rice cultivation. Alternatively, in years when an early onset was observed, late planting in the season reduced the use of rain water by 95% while increasing the irrigation water requirement by 11% compared with planting at rainfall onset. Access to supplementary with AWD irrigation increased the stability of grain yield, and crop and water productivity, irrespective of the onset of rainfall or time of crop establishment.