The use of net ecosystem exchange (NEE) data to estimate carbon transfer coefficients is investigated in the context of a deterministic compartmental carbon sequestration system. Sensitivity and approximation properties are investigated for the underlying model initial value problems. Joint probability distributions are obtained by including NEE data along with corresponding synthetic NEE values generated from the model and are compared with a priori distributions. These distributions are used to estimate individual transfer parameters and to predict future carbon states. Results are compared with those obtained using only a priori information without the benefit of data. Shannon information content is introduced to measure the dependence of results on the lengths of observational intervals and provide an additional indicator of the value added by the inclusion of NEE data.