ABSTRACT: The current paradigm in wetland ecology is that shallow systems are fully mixed, at least vertically. However, detailed measurements of stratification in coloured wetlands show that they can be stratified for several days at a time. These timescales of stratification will in turn have a profound impact on the wetland ecology. This study aimed to test the ability of hydrodynamics models, originally developed for deep lakes, to predict the hydrodynamics of shallow systems. The stratification in a shallow wetland is strongly influenced by the effects of the margins; areas which have small impact on the overall hydrodynamics and stratification of lakes. Thus, the relatively coarse treatment of margins in existing models impedes their direct application to wetlands. The lake models, 3D-ELCOM and 1D-DYRESM, were transformed for use in wetlands, then used to investigate the effect of changing water levels on wetland stratification cycles and hydrodynamics. In particular, we investigated the interactions between water level and colour in determining those stratification timescales. We also found that we were able to predict the increase in the degree and duration of stratification as water colour intensified.