A modal analysis in the horizontal plane was extended to a layer-stratified basin with irregular bathymetry, and the theory was applied to Lake Biwa to investigate the horizontal structure and excitation of the basin-scale internal waves and gyres. The horizontal structure of the basin-scale internal waves consisted of cyclonic and anticyclonic elliptic cells, each of which appeared to follow the dispersion relationship of Kelvin and Poincare waves in elliptic basins. The internal waves were preferentially excited depending on the arrangement of the cells and the wind direction, but the spatial distribution of wind stress curl over the lake primarily determined the horizontal structure of the ensuing gyres. Decoupled evolutionary equations for the individual modes provided a good approximation for excitation of the internal waves and early stages of excitation of the gyres before nonlinear effects and damping become significant. The modal decomposition of hydrodynamic simulation results also showed that the primary action of the wind was to excite the internal waves; however, these internal waves were damped within a few days, and the dynamics during calm periods were dominated by the gyres, illustrating the importance of internal waves on mixing and gyres on long-term horizontal transport.