Floodplain wetlands support enormous biodiversity and range of other vital ecosystem services. However, these wetlands are threatened by a range of processes. In the Murray-Darling system of southeast Australia, these processes include altered wetting regimes, cropping, grazing, invasive species and even forestry. Detecting and monitoring changes to these systems is limited by poor benchmark data, which would otherwise provide the basis for establishing the degree and nature of changes as well as possible drivers. This study sought to establish benchmark conditions and temporal patterns of change in wetland plant communities by examining stratigraphic changes in germination patterns from the wetland seed banks, taking advantage of the capacity in many wetland plants for seeds to remain viable in the sediment for many years and to subsequently germinate upon wetting. Sediments from 12 wetlands in the Koondrook-Perricoota Forest were sampled at 2 cm intervals to depths of 30 cm to 40 cm. These sediments were subject to a wetting trial in a greenhouse over 15 weeks to establish the germinant assemblages of each wetland and depth sample. Lead-210 dating of the sediment profiles suggest the upper 10 to 16 cm of these sediment sequences were deposited in the last 100 years. More than 2200 seedlings from 20 taxa were identified from the samples. General patterns of decline in seedling abundance, richness and diversity with depth were observed, consistent with expected age-depth declines in seed viability. However, deviations from this expected pattern of decline with depth were observed in some wetlands and for some taxa, suggesting the abundance, richness and diversity of the seed bank has declined in the last century. These findings provide support for the hypothesis that floodplain wetland plant communities have been negatively affected by the changes to land and river management following displacement of indigenous peoples by British colonisers.