Abstract Hypoxic floodwaters can seriously damage seedlings. Seed dormancy could be an effective trait to avoid lethal underwater germination. This research aimed to discover novel adaptive dormancy responses to hypoxic floodwaters in seeds of Echinochloa crus‐galli, a noxious weed from rice fields and lowland croplands. Echinochloa crus‐galli dormant seeds were subjected to a series of sequential treatments. Seeds were: (i) submerged under hypoxic floodwater (simulated with hypoxic flasks) at different temperatures for 15 or 30 days, and germination tested under drained conditions while exposing seeds to dormancy‐breaking signals (alternating temperatures, nitrate (KNO3), light); or (ii) exposed to dormancy‐breaking signals during hypoxic submergence, and germination monitored during incubation and after transfer to drained conditions. Echinochloa crus‐galli seed primary dormancy was attenuated under hypoxic submergence but to a lesser extent than under drained conditions. Hypoxic floodwater did not reinforced dormancy but hindered secondary dormancy induction in warm temperatures. Seeds did not germinate under hypoxic submergence even when subjected to dormancy‐breaking signals; however, these signals broke dormancy in seeds submerged under normoxic water. Seeds submerged in hypoxic water could sense light through phytochrome signals and germinated when normoxic conditions were regained. Hypoxic floodwaters interfere with E. crus‐galli seed seasonal dormancy changes. Dormancy‐breaking signals are overridden during hypoxic floods, drastically decreasing underwater germination. In addition, results indicate that a fraction of E. crus‐galli seeds perceive dormancy‐breaking signals under hypoxic water and germinate immediately after aerobic conditions are regained, a hazardous yet less competitive environment for establishment.