The Great Lakes are subject to coastal flooding as a result of severe storms. Strong winds blowing across the surface of the lakes produce high waves and surge. Variations in lake levels due to decadal scale variations in precipitation and anthropogenic activities affect the risk of flooding. In this report, historical storm climatology on Lakes Michigan and St Clair, and the resulting measured waves and water levels, are analyzed in detail. The physical processes that produce coastal flooding are investigated. The detailed history of water level and wave time series and associated probabilities are calculated, with long term, seasonal, and event time scales analyzed separately. Various parametric correlations between time scales and between spatial locations are quantified. A flood map methodology is proposed that improves the accuracy of base flood elevation prediction and improves the uncertainty prediction. The methodology takes full advantage of the latest storm wave and water level hydrodynamic modeling capabilities, as well as long term meteorological, ice, wave, and water level measurements.