Yield advantages of crops grown behind windbreaks have often been reported, but underlying principles responsible for such changes and their long-term consequences on crop productivity and hence farm income have rarely been quantified. Physiologically and physically sound simulation models could help to achieve this quantification. Hence, the APSIM systems model, which is based on physiological principles such as transpiration efficiency and radiation use efficiency (termed here APSIMTE), and the Soil Canopy Atmosphere Model (SCAM), which is based on the Penman–Monteith equation but includes a full surface energy balance, were employed in developing an approach to quantify such windbreak effects. This resulted in a modified APSIM version (APSIMEO), containing the original Penman equation and a calibration factor to account for crop- and site-specific differences, which were tested against field data and simulations from both the standard APSIMTE and SCAM models. The APSIMEO approach was tested against field data for wheat and mungbean grown in artificial enclosures in south-east Queensland and in south-east Western Australia. For these sheltered conditions, daily transpiration demand estimates from APSIMEO compared closely to SCAM. As the APSIMEO approach needed to be calibrated for individual crops and environments, average transpiration demand for open field conditions predicted by APSIMEO for a given site was adjusted to equal that obtained using APSIMTE by modifying a calibration parameter β. For wheat, a β-value of 1.0 resulted in best fits for Queensland, while for Western Australia a value of 0.85 was necessary. For mungbean a value of 0.92 resulted in the best fit (Qld). Biomass and yields simulated by APSIMTE and the calibration APSIMEO for wheat and mungbean grown in artificial enclosures were generally distributed around the 1:1 line, with R2 values ranging from 0.92 to 0.97. Finally, APSIMEO was run at 2 sites using long-term climate data to assess the likely year-to-year variability of windbreak effects on crop yields. Assuming a 70% reduction in wind speed as representing the maximum potential windbreak effect, the average yield improvement for the Queensland site was 13% for wheat and 3% for mungbean. For wheat at the WA site the average yield improvement from reduced wind speed was 5%. In any year, however, effects varied from negative, neutral to positive, highlighting the highly variable nature of the expression of windbreak effects. This study has shown how physical and biological modelling approaches can be combined to aid our understanding of systems processes. Both the environmental physics perspective and the biological perspective have shortcomings when issues that sit at the interface of both approaches need to be addressed. While the physical approach has clear advantages when investigating changes in physical parameters such as wind speed, vapour pressure deficit (VPD), temperature or the energy balance of the soil–plant–atmosphere continuum, it cannot deal with complex, biological systems adequately. Conversely, the crop physiological approach can handle such biological interactions in a scientific and robust way while certain atmospheric processes are not considered. The challenge was not to try and capture all these effects in 1 model, but rather to structure a modelling approach in a way that allowed for inclusion of such processes where necessary.