In this work we discuss applications of Lagrangian techniques to study transport properties of flows generated by shallow water models of estuarine flows. We focus on the flow in the Chesapeake Bay generated by Quoddy (see Lynch and Werner, 1991), a finite-element (shallow water) model adopted to the bay by Gross et al. (2001). The main goal of this analysis is to outline the potential benefits of using Lagrangian tools for both understanding transport properties of such flows, and for validating the model output and identifying model deficiencies. We argue that the currently available 2-D Lagrangian tools, including the stable and unstable manifolds of hyperbolic trajectories and techniques exploiting 2-D finite-time Lyapunov exponent fields, are of limited use in the case of partially mixed estuarine flows. A further development and efficient implementation of three-dimensional Lagrangian techniques, as well as improvements in the shallow-water modelling of 3-D velocity fields, are required for reliable transport analysis in such flows. Some aspects of the 3-D trajectory structure in the Chesapeake Bay, based on the Quoddy output, are also discussed.