Unlike most crops, rice is flooding tolerant and this feature has been exploited for weed management in rice fields. Flooding of rice fields prevents weed establishment, while rice remains unaffected. However, the recent emergence of certain endemic weed species adapted to submergence has decreased the effectiveness of this weeding method. Studying these weeds is important both for devising alternative weed management strategies and to better understand plant flood adaptation, to uncover associated genetic mechanisms. For our study, Echinochloa crus-galli, often referred to as one of the worst weeds worldwide and highly submergence tolerant, was selected together with an intolerant maize cultivar and two rice varieties (one tolerant and one intolerant). Flooding resilience in the tolerant weed and in the tolerant rice is achieved by different means. Time-course transcriptomics analyses indicated many commonly regulated genes but also revealed crucial mechanisms associated with differential growth and metabolic responses to both underwater stress (hypoxia and reduction of light) and post-submergence stress (reoxygenation and re-illumination). A comparative analysis of the weed genome composition to 17 other grass species revealed a conservation of flooding responses in the grass family, as well as species-specific flooding tolerance responses in the weed. This could have been acquired by a relatively recent exposure to flooded conditions. Greenhouse and field experiments showed that weed management protocols using early flooding followed by natural shade from high shade-casting rice cultivars might be the most efficient way to both naturally suppress weed growth in rice fields and preserve fresh water resources.