Internal seiches play a significant role in a broad range of physical, chem
ical, and biological processes in lakes. A detailed assessment of the impac
t of seiching requires an understanding of seiche structure, which is deter
mined by bathymetry and stratification. In this study, internal seiche solu
tions are evaluated for arbitrary bathymetry and continuous stratification
using a two-dimensional numerical model. Formulated in terms of a stream fu
nction, the model produces a finite set of linear internal wave eigenmodes
and allows the computation of the complete velocity field (over a grid) ass
ociated with each seiche mode. Several idealized configurations of continuo
us 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 flux
es, sediment transport, and internal wave damping. Model results are also c
ompared to thermistor chain data collected in the Upper Mystic Lake (UML, W
inchester, Massachusetts). Using an idealized description of the UML bathym
etry and density profiles which emulate the seasonal variation of stratific
ation in the lake, the evolution of bed velocities during the autumnal brea
kdown in stratification is assessed, providing insight into the fate of the
contaminants entering the lake.