The distribution of woody plant in wetlands may be influenced by topographic microsites that differ in flooding duration, substrate composition, moisture retention, canopy cover, nutrient availability, and seed trapping ability. In order to assess the effects of microsites on woody plant regeneration in Bonita Swamp, a wetland in Western New York, we conducted an assessment of 15 microsite types, a survey of 400 trees, and a woody seedling count using nineteen 100 m² quadrats in a 4.3 ha study area. Acer × freemanii E.Murr., Fraxinus pennsylvanica Marshall, and Ulmus americana L. dominated the overstory and the often inundated swales occupied 50.3% of the soil surface. Relative to area occupied by each microsite, seedlings were found more often than expected on elevated moss, near elevated moss/soil, near log/root, and swale microsites with 66% of woody seedlings occurring in swales. Acer × freemanii and Fraxinus pennsylvanica occurred more often than expected in the swales. Seedlings appear to prefer moss substrates over soil and wood substrates. Hydrochory may explain the preference of seedlings for “near” microsites onto which wind, water currents and receding spring flood waters deposit floating seeds. Mean percent canopy cover did not vary over the different microsite types, over different species, or between the first and second year (or older) seedlings. Woody seedlings that were two years old or older were found at significantly higher relative elevations and were much less frequent than first year seedlings indicating high mortality and the importance of elevation to survival and establishment. The elevations of microsites are important to woody plant regeneration in this system.