• Improvements in ORYZA (v3) were identified and compared to ORYZA2000. • Soil carbon, nitrogen, and temperature dynamic modules were developed. • Algorithms for the effects of environmental stresses on rice growth were improved. • Case studies confirmed successful improvement of the model.

• Rice crop responses to soil salinity can be fitted with a logistic function with three parameters. • Tolerant genotype, BRRI Dhan 47 presented 50% of reduction in leaf net photosynthesis and transpiration at soil salinity higher than 14 dS m−1. • Growth of tolerant genotype as BRRI Dhan 47 was significantly reduced at soil salinity higher than 5 dS m−1.

• ORYZA v3 and APSIM-Oryza models were improved to account for salinity effects on rice production. • Variability of soil salinity was represented by a simple linear relationship between salt concentration and electrical conductivity. • The derived salinity parameters captured response differences between tolerant (BRRI Dhan47) and non-tolerant variety (IR64). • An increase in salinity parameters of 5 % above the value for IR64 would result in a 3 % increase in simulated yield.