The objectives of this study were to assess Zn status of soils in Fars, Isfahan and Qom provinces of Iran , to model the relationship between wheat and rice grain Zn and agro-ecosystem parameters, to calculate the Zn fluxes from soil into plants and modeling accumulation rate of Zn in the agro-ecosystems of study area. About 222 soil (0-30 cm) and plant (wheat and rice) samples were collected randomly from the agricultural soils. Linear regression models were fitted by least square and robust methods to model soil Zn and grain Zn (of wheat and rice) and agro-ecosystem parameters relationships. Zinc fluxes from soil to plants and Zn accumulation rates in the agro-ecosystems were computed using mass flux assessment (MFA) model. Agricultural information was used to quantify Zn fluxes and Zn accumulation rate. The results indicated that total Zn concentration of soils were in normal ranges and the DTPA extractable Zn concentrations were above the critical levels in 84% of the surveyed fields. Zinc concentration of wheat grains was mostly sufficient with respect to plant nutrition but its bioavailability for consumers was generally low in more than 75% of the samples because of high phytic acid to Zn molar ratio. The regression analysis showed that Zn status of agricultural soils and wheat grains could be expressed as a function of soil properties and other ecosystem parameters on a regional scale. Zinc mass fluxes from soil to grains were in range of 62-158 g ha -1 yr -1 and 69-120 g ha -1 yr -1 for wheat and rice, respectively. Modeling Zn accumulation rate indicated that Zn is accumulating considerably in the agricultural soils of the study region. The major Zn input routes to the agricultural soils are manure and mineral fertilizers on the regional scale. Keywords : Modeling, Zn flux, Agro-ecosystem, Znic accumulation rate.