Weeds threaten food security. Yet their survival in the modern agroecosystem, where they face strong natural and anthropogenic selection, demonstrates they possess remarkable resilience. If our crops of the future posed these resilience traits, they would withstand climate change better. Black-grass (Alopecurus myosuroides) is one of the most problematic and damaging agricultural weeds in Western Europe’s winter wheat (Triticum aestivum) and other crops. Previous studies link black-grass patches to water-retaining soils, but its specific adaptations to these conditions were unknown. To address this knowledge gap, we conducted pot-based waterlogging experiments comparing the waterlogging tolerance between wheat and blackgrass. Sampling thirteen blackgrass biotypes and six wheat cultivars, we observed that waterlogged wheat produced less aerial tissue biomass, while black-grass maintained or increased aerial tissue production. As expected, waterlogged wheat roots induced aerenchyma whereas surprisingly, aerenchyma-like structures were constitutively present in black-grass. To gain a molecular-level understanding of waterlogging responses within and between these species, we performed matched transcriptomic and metabolomic analyses from leaves of control or waterlogged plants. In wheat, transcripts associated with regulation and utilisation of phosphate compounds were upregulated, and concentrations of sugars and amino acids increased. Black-grass biotypes showed limited molecular responses to waterlogging, with some black-grass amino acids decreasing. Of the few blackgrass transcripts that changed, the one standout was a gene identified in screens for genes underpinning metabolism-based resistance to herbicides. Our findings provide valuable insights into the different waterlogging tolerances of these species and gives a mechanistic understanding of blackgrass’s patchy distribution in wheat fields.