Agricultural flooding causes tens of billions of dollars in annual losses globally, yet the methods used to assess these losses systematically capture only a fraction of their true economic scope. This systematic review synthesizes 65 peer-reviewed studies published between 1984 and 2025 to evaluate how agricultural flood damage is measured, what damage categories are covered, and where critical methodological gaps persist. We find a structural asymmetry across the reviewed literature – all 65 reviewed studies address direct immediate damages – primarily crop yield loss estimated through depth-damage functions or remote sensing – while direct induced effects appear in only 8 studies, indirect damages in 9, and intangible damages in fewer than 5. This asymmetry has persisted for four decades, through a major remote sensing revolution, because the dominant methods are structurally incapable of measuring damage categories beyond direct immediate losses. We introduce a Methods-by-Damage-Category Matrix that maps eight assessment methods against five damage categories, making the coverage gap visible and providing a diagnostic framework for method selection. Three post-2013 damage frontiers – long-term land productivity degradation, supply chain finance disruption, and farmer mental health – are identified as emerging categories warranting dedicated methodological development. Existing agricultural flood damage estimates used in benefit–cost analyses and disaster compensation are systematically downward-biased; closing this bias requires integrating remote sensing-based physical detection with economic valuation methods capable of capturing the full damage taxonomy.