Mudflats are exposed for short periods after flood water drawdown. They support fast-growing annual herbs with a ruderal strategy. To optimize their recruitment success, seeds of mudflat species germinate better under fluctuating temperatures, full illumination and aerobic environments that indicate the presence of optimal (non-flooded) conditions for plant growth and development. Here, we hypothesize that prior exposure of mudflat seeds to hypoxic (flooded) environment interferes with the germination process and results in more vigorous germination once aerobic conditions are regained. To test this hypothesis, seeds of five mudflat species were incubated in both aerobic and hypoxic environments at four (14/6, 22/14, 22/22 and 30/22°C) temperature regimes, reflecting different (seasonal) conditions when drawdowns may occur. All species responded positively to four temperature regimes; however, moderate 22/14 and 22/22°C temperatures were optimum for high percentages and rates (speed) of seed germination. Since seeds of four species germinated exclusively under aerobic conditions, they were moved from hypoxic to aerobic conditions. Prior exposure of seeds to hypoxic environment facilitated high percentages, rates and synchronization of germination of Limosella aquatica, Peplis portula and Samolus valerandi seeds compared to incubation under strict aerobic conditions. However, prior exposure to hypoxic environment induced secondary dormancy in non-dormant seeds of Hypericum humifusum but broke dormancy in Lythrum hyssopifolia seeds that otherwise required cold stratification to overcome physiological dormancy. All species that have a narrow ecological niche (strictly occurring in mudflat habitats) showed positive responses to prior exposure to hypoxic environments. In contrast, H. humifusum that has a wide ecological niche (from mudflats to moist sandy grasslands) showed a negative response. We conclude that the hypoxic environment may strongly affect seed germination behaviour once the aerobic environment is regained. The most striking effect is the acceleration of the germination process and, therefore, life cycle supporting the survival in an ephemeral habitat.