Information about potential scenarios and causes of floods is important for future planning. Historical weather data of Fredericton (New Brunswick) and Charlottetown (Prince Edward Island), the two coastal cities of Atlantic Canada, were analyzed using RClimDex, Mann–Kendall test, and Sen’s slope estimates for potential scenarios and causes of floods. Flood hazard analyses were conducted using GIS (Geographical Information System) and ArcSWAT software. The watersheds of Fredericton and Charlottetown were delineated from 25 × 25 m resolution DEMs (Digital Elevation Models) of the two cities followed by percent watershed area calculations for different elevation classes for flood generation. Over the past 100 years, there was a significant decreasing trend in the high intensity precipitation in Charlottetown supported by a significant decrease in the number of heavy precipitation days. However, maximum one-day precipitation and maximum five-day precipitation significantly increased in Charlottetown and Fredericton, respectively. Charlottetown received more annual precipitation than Fredericton. In the last 30 years, there was an event exceeding 50 mm precipitation (considered as a threshold for the return period of urban floods) in Charlottetown; Fredericton experienced such events for more than 1.5 times. For twelve times, these events occurred more than once in a year in Charlottetown as compared to fourteen times in Fredericton. Despite statistically proven similarities in the occurrence of extreme events in the two cities, the visualized flood hazards, and the mapping of watershed characteristics, no devastating floods were reported for Charlottetown. This does not necessarily mean that there had never been risks of flooding in Charlottetown. These findings may help policymakers for future developments.