Lake of the Woods spans two geological regions: the Precambrian Shield and the Glacial Lake Agassiz Lakebed. The lake watershed’s complex topography influences wind speeds and directions. We study wind variability over Lake of the Woods using reanalysis data and wind observations at seven sites. A wind variability index is proposed as a measure of lake-wide spread in wind direction. Our results show that the directional variability depends on wind speeds, with higher variability at lower speeds. The wind variability also changes throughout the year; it is more pronounced in spring (Apr-Jun) and fall (Sep-Oct) and less pronounced during winter (Dec-Jan). Observed wind directions are 60% more variable than reanalysis wind, indicating a need for higher-resolution reanalysis to resolve local wind effects due to topographic changes. Based on the statistical hierarchical clustering method, our analysis shows that geographically variable wind can be grouped into three regions to represent the predominant wind directions accurately. Clustering results also suggest spatial coverage gaps in the existing meteorological observation network. We reassess the existing network and propose a new meteorological observation site in the southeast basin near Morson, Ontario. Our study is of significance for water quality management because the wind is the key driver of water circulation, transport, and mixing in the lake, and accurate wind measurements are necessary to better constrain the underpinning physical, biological, and biochemical processes in mechanistic ecological models.