In an idealized situation of a baroclinically unstable single eddy, we study the impact of eddy-induced mixing on the soft-tissue carbon pump. The new element here is the coupling of a three-dimensional nonhydrostatic ocean model with a physiological plankton model that is able to represent a variable plankton C:N ratio. During the development and breakup of the eddy, a complicated vertical velocity field appears. The processes of transport and plankton growth, as well as the effect of the flow on the C:N ratio, are studied in detail. The physical processes associated with eddy breakup have a strong impact on the local environment in which the plankton grows. The changes in the local environment lead to a decrease of the C:N ratio (about 30% throughout the upper 150 m of the domain) and hence a weakening of the soft-tissue carbon pump. According to a sensitivity analysis, the decrease of the C:N ratio as a consequence of the flow field appears robust; it does not depend on specific parameter values in the model. Copyright 2007 by the American Geophysical Union.