Brent geese Branta bernicla spring fattening around Agerø, Denmark, alternate between feeding on saltmarshes and submerged Zostera beds in Limfjorden. It appeared from field observations that these alternations depended on the water level in Limfjorden. A model was developed to assess the impact of water level fluctuations on the habitat use. A second model was developed to estimate the impact of water level on Zostera availability. The first model was successful in demonstrating that fluctuations in water levels had considerable influence on habitat use by the brent geese, i.e. they fed on Zostera at low water levels and on saltmarshes during high water levels, particularly so in early spring, and that the switch between habitats occurred within a narrow water level span of ca 30 cm. The second model demonstrated that the switch between habitats could be explained by lowered availability of Zostera as water levels increased. By combining the output from the two models, differences between years could partly be explained by differences in Zostera availability in the early spring period (21 March ‐ 25 April), whereas a more complicated situation was detected later in spring (26 April ‐ 31 May). The models presented may be considered as tools in investigations of habitat use and carrying capacity of seagrass beds in non‐tidal areas, where birds' access to feeding areas regularly may be hindered by high water levels.