Internal seiches play a significant role in a broad range of physical, chemical, and biological processes in lakes. A detailed assessment of the impact of seiching requires an understanding of seiche structure, which is determined by bathymetry and stratification. In this study, internal seiche solutions are evaluated for arbitrary bathymetry and continuous stratification using a two-dimensional numerical model. Formulated in terms of a stream function, the model produces a finite set of linear internal wave eigenmodes and allows the computation of the complete velocity field (over a grid) associated with each seiche mode. Several idealized configurations of continuous stratification and variable bathymetry are used to explore the effect of nonuniform systems on internal wave structure. In particular, we focus on bed velocity distribution and the resulting potential impact on scalar fluxes, sediment transport, and internal wave damping. Model results are also compared to thermistor chain data collected in the Upper Mystic Lake (UML, Winchester, Massachusetts). Using an idealized description of the UML bathymetry and density profiles which emulate the seasonal variation of stratification in the lake, the evolution of bed velocities during the autumnal breakdown in stratification is assessed, providing insight into the fate of the contaminants entering the lake. ¿ 2000 American Geophysical Union