Changes in climate, food abundance and disturbance from humans threaten the ability of species to successfully use stopover sites and migrate between non‐breeding and breeding areas. To devise successful conservation strategies for migratory species we need to be able to predict how such changes will affect both individuals and populations. Such predictions should ideally be process‐based, focusing on the mechanisms through which changes alter individual physiological state and behavior. In this study we use a process‐based model to evaluate how Black Brant (Branta bernicla nigricans) foraging on common eelgrass (Zostera marina) at a stopover site (Humboldt Bay, USA), may be affected by changes in sea level, food abundance and disturbance. The model is individual‐based, with empirically based parameters, and incorporates the immigration of birds into the site, tidal changes in availability of eelgrass, seasonal and depth‐related changes in eelgrass biomass, foraging behavior and energetics of the birds, and their mass‐dependent decisions to emigrate. The model is validated by comparing predictions to observations across a range of system properties including the time birds spent foraging, probability of birds emigrating, mean stopover duration, peak bird numbers, rates of mass gain and distribution of birds within the site: all 11 predictions were within 35% of the observed value, and 8 within 20%. The model predicted that the eelgrass within the site could potentially support up to five times as many birds as currently use the site. Future predictions indicated that the rate of mass gain and mean stopover duration were relatively insensitive to sea level rise over the next 100 years, primarily because eelgrass habitat could redistribute shoreward into intertidal mudflats within the site to compensate for higher sea levels. In contrast, the rate of mass gain and mean stopover duration were sensitive to changes in total eelgrass biomass and the percentage of time for which birds were disturbed. We discuss the consequences of these predictions for Black Brant conservation. A wide range of migratory species responses are expected in response to environmental change. Process‐based models are potential tools to predict such responses and understand the mechanisms which underpin them.