The upwind model is well known to simulate shockwaves, but it is rarely applied to natural rivers because of problems caused by the source terms. Although several methods have been developed to deal with the source terms, none of them has been applied to natural rivers. This paper deals with application of the upwind model to the natural river. An implicit upwind model is applied to a hypothetical irregular channel and a natural river with highly irregular bed, width, and hydraulic structures. Different types of the flows including steady-state flow, flood wave, dam-break wave, and bore are simulated to test accuracy and applicability of the implicit upwind model. It is proved that the model can simulate various types of flows in natural rivers with high accuracy and robustness.