We developed a high-resolution (250 m) three-dimensional hydrodynamic model of Lake of the Woods (LoW) to study surface seiches, lake circulation, and water temperature. LoW spans over two different geological regions, experiences wind variability, encompasses >14,500 islands and includes twelve hydraulically connected sub-basins. The complex geometry and topography are unique for this large lake that suffers from seasonal algal blooms. The model uses a spatially and temporally variable wind field, heat fluxes, riverine inflows obtained from a watershed model, outflows at Kenora and Norman dams, and was run for the spring-summer of 2017 and 2018. The predominant physical processes in LoW are surface seiches, and wind and rivers drive mean lake-wide circulations and mixing. The observed periods of seiches in the lake are 9.5, 3.4, 2.3, and 1.3 h, attributed to horizontal modes 1, 3, 6, and 12, respectively. Amphidromic structures show that sub-basin seiche's responses to wind may be limited to one sub-basin; however, lake-wide responses were also observed, which suggests the seiche-induced oscillatory velocities can impact transport paths. The mean water temperature is variable spatially, ranging from <15 °C in early June to ∼25 °C in July-August. Sabaskong Bay experienced warmer summer water temperatures with unidirectional mean flows to the lake. Main water transport is towards the northeast. Modelled conservative tracers, consistent with observations, show that the Rainy River plume extent covers Big Traverse, Morson, and Little Traverse Bays. The modelled seasonal hydraulic retention times in southern bays are <150 days and are much longer in northern bays.