Wind driven oscillations of water surfaces (surface seiches) are a key driver of ecological fluxes, such as of oxygen and nutrients, within lakes and reservoirs. These seiches exhibit low frequency oscillations with periods typically in the range from minutes to days, closely-spaced modes and a low signal to noise ratio, which makes modal analysis by simple spectral techniques challenging. Time domain operational modal analysis, specifically the Random Decrement Technique, was applied to extract modal parameters for the dominant surface seiches of Lake Geneva, Switzerland, and Lake Tahoe, USA. The results obtained show good agreement with existing literature on the periods and damping ratios of the seiches, historically obtained in this field by visual selection of free-decay sections of the time series or half-power peak picking. These analyses illustrate the potential for the use of techniques developed for operational modal analysis in areas outside the realm of mechanical and civil structures dynamics.