Models are key tools in our quest to better understand the impacts of soil waterlogging on plant growth and crop production. Here, we reviewed the state of the art of modeling approaches and compared the conceptual design of these models with recent experimental findings. We show that many models adopt an aeration stress (AS) principle where surplus water reduces air‐filled porosity, with implications for root growth. However, subsequent effects of AS within each model vary considerably. In some cases, AS inhibits biomass accumulation (e.g. AquaCrop), altering processes prior to biomass accumulation such as light interception (e.g. APSIM), or photosynthesis and carbohydrate accumulation (e.g. SWAGMAN Destiny). While many models account for stage‐dependent waterlogging effects, few models account for experimentally observed delays in phenology caused by waterlogging. A model intercomparison specifically designed for long‐term waterlogged conditions (APSIM‐Oryza) with models developed for dryland conditions with transient waterlogging would advance our understanding of the current fitness for purpose of exsiting frameworks for simulating transient waterlogging in dryland cropping systems. Of the point‐based dynamic models examined here, APSIM‐Soybean and APSIM‐Oryza simulations most closely matched with the observed data, while GLAM‐WOFOST achieved the highest performance of the spatial‐regional models examined. We conclude that future models should incorporate waterlogging effects on genetic tolerance parameters such as (1) phenology of stress onset, (2) aerenchyma, (3) root hydraulic conductance, (4) nutrient‐use efficiency, and (5) plant ion (e.g. Fe/Mn) tolerance. Incorporating these traits/effects into models, together with a more systematic model intercomparison using consistent initialization data, will significantly improve our understanding of the relative importance of such factors in a systems context, including feedbacks between biological factors, emergent properties, and sensitive variables responsible for yield losses under waterlogging.