During flooding, crops can lose the battle for resources to highly competitive weeds. One example is Echinochloa crus-galli that greatly reduces the yields of rice as well as those of crops in flood-susceptible fields. We analyzed if hypoxia, caused by flooding, impacts seed primary dormancy attenuation or secondary dormancy induction in an E. crus-galli population resistant to anaerobic germination. We also aimed at gaining a deeper insight into the alternating temperature requirement for dormancy breaking, considered a wetland plants trait to avoid lethal underwater germination. Seed lots with two contrasting dormancy levels were evaluated, i) non-deep dormant seeds (after-ripened) and ii) dormant seeds (freezer-stored). Seeds of both lots were submerged in hypoxic floodwaters (2.5 to 3.0 kPa pO2) for 15-30 days, later incubated under drained conditions and exposed to dormancy-breaking signals (light, daily alternating temperatures, and nitrates). We found that during flooding, seeds primary dormancy was less attenuated compared to the control treatment. On the other hand, non-deep dormant seeds did not reinforce dormancy under hypoxia at winter temperatures (10°C). Remarkably, hypoxic floodwaters prevented the induction of secondary dormancy triggered by continuously high temperatures (>25°C). These findings suggest that flooding delays primary dormancy attenuation during cold periods and inhibits secondary dormancy induction during warm periods. Moreover, exposing seeds to dormancy-breaking cues did not release germination from the inhibitory effects of hypoxic floodwaters. However, in the E. crus-galli population studied, the expression of dormancy under a normoxic (19.9 to 21.2 kPa pO2) water table allows seeds to avoid underwater germination. In conclusion, results suggest that floodwaters can affect seed dormancy transitions and, thus, germination timing in the field.