Abstract. Standing surface waves or seiches are inherent hydrodynamic features of enclosed water bodies. Their two-dimensional structure is important for estimating flood risk, coastal erosion, and bottom sediment transport, and for understanding shoreline habitats and lake ecology in general. In this work, we present analysis of two-dimensional seiche characteristics in Flathead Lake, Montana, USA, a large intermountain lake known to have high seiche amplitudes. To examine spatial characteristics of different seiche modes, we used the original procedure of determining the seiche frequencies from the primitive equation model output with subsequent derivation of the spatial seiche structure at fixed frequencies akin to the tidal harmonic analysis. The proposed procedure revealed specific seiche oscillation features in Flathead Lake, including maximum surface level amplitudes of the first fundamental mode in straights around the largest island; several higher modes appearing locally in the vicinity of the river inflow; the "Helmholtz" open harbor mode, with the period approximately twice that of the longest seiche mode, generated by a large shallow bay connected to the main lake basin; and several rotating seiche modes potentially affecting the lake-wide circulation. We discuss lake management problems related to the spatial seiche distribution, such as shoreline erosion, floods, and transport of sediments and invasive species in Flathead Lake.