Despite the development of advanced process-based methods for estimating the discharge capacity of vegetated river channels, most of the practical one-dimensional modeling is based on a relatively simple divided channel method (DCM) with the Manning flow resistance formula. This study is motivated by the need to improve the reliability of modeling in practical applications while acknowledging the limitations on the availability of data on vegetation properties and related parameters required by the process-based methods. We investigate whether the advanced methods can be applied to modeling of vegetated compound channels by identifying the missing characteristics as parameters through the formulation of an inverse problem. Six models of channel discharge capacity are compared in respect of their uncertainty using a probabilistic approach. The model with the lowest estimated uncertainty in explaining differences between computed and observed values is considered the most favorable. Calculations were performed for flume and field settings varying in floodplain vegetation submergence, density, and flexibility, and in hydraulic conditions. The output uncertainty, estimated on the basis of a Bayes approach, was analyzed for a varying number of observation points, demonstrating the significance of the parameter equifinality. The results showed that very reliable predictions with low uncertainties can be obtained for process-based methods with a large number of parameters. The equifinality affects the parameter identification but not the uncertainty of a model. The best performance for sparse, emergent, rigid vegetation was obtained with the Mertens method and for dense, flexible vegetation with a simplified two-layer method, while a generalized two-layer model with a description of the plant flexibility was the most universally applicable to different vegetative conditions. In many cases, the Manning-based DCM performed satisfactorily but could not be reliably extrapolated to higher flows.