A hybrid surface/subsurface flow and transport model is developed that blends distributed parameter models with simpler lumped parameter models. The hybrid model solves the channel flow and saturated groundwater flow domains in continuous time using fully distributed physically-based formulations. This system is supplemented with the overland flow and unsaturated groundwater flow that uses lumped parameter descriptions in discrete time. In the proposed model, a one-dimensional channel flow model is dynamically coupled with a two-dimensional vertically-averaged groundwater flow model along the river bed. As an alternative to the commonly applied iterative solution technique, a so-called simultaneous solution procedure is developed to provide a better understanding to the coupled flow problem. This new methodology is based on the principle of solving the two flow domains within a single matrix structure in a simultaneous manner. In addition to the flow model, a coupled contaminant transport model is also developed to simulate the migration of contaminants between surface and subsurface domains. The contaminant transport model dynamically couples a one-dimensional channel transport model with a two-dimensional vertically-averaged groundwater transport model. The coupling is performed at the river bed interface via advective and dispersive transport mechanisms. A modified extension of the proposed simultaneous solution procedure is also implemented to solve the coupled contaminant transport problem. The dynamic coupling provides the much needed understanding for the continuity of contaminants in strongly interacting surface/subsurface systems such as a river and an unconfined aquifer. The coupled flow and transport models are applied to the lower Altamaha watershed in southern Georgia. The flow model is used to perform simulations of hydrologic and hydraulic conditions along the river and in the dynamically linked surfacial aquifer. The model predicted the flood patterns including the magnitude of peaks and their arrival times with accuracy. Under the given flow conditions, the transport model is then implemented to test alternative contaminant transport patterns both in the river and within the aquifer. It has been found that the channel network would serve as a conduit for rapid transport of contaminants within the aquifer to large distances in small time frames.