Hydrological connectivity regulates CO2 and CH4 emissions from a temperate, natural river-floodplain system

Natural river-floodplains are significant sources of greenhouse gases (GHG) including CO₂ and CH₄, yet the role of hydrological connectivity in shaping aquatic fluxes of these gases (FCO2 and FCH4) remains unclear. This study was conducted in a temperate river-floodplain system (Poland), using manual and automated flux chambers where we measured 1776 FCH4 and 1783 FCO2 during various water levels in 15 locations across dormant and growing seasons.The system showed a high spatio-temporal variability, with the highest FCH4 in the disconnected sidearms and the highest FCO₂ in the river. Hydrology strongly regulated FCO2, while FCH4 responses were jointly shaped by temperature, connectivity and local hydrological conditions. The system was the strongest source of GHGs (in CO2-equivalent; CO2-eq) in the summer and the weakest in the spring. Over the last ten years (2015–2025), significantly more of the CO2-eq was emitted during the growing seasons, despite a larger aquatic floodplain area during the dormant seasons. This study highlights that accounting for hydrological diversity is crucial to avoid bias in estimates of aquatic GHG balances, even in nearby physicochemically similar systems. This research fills a key gap in hydrological controls of FCO2 and FCH4 in natural river-floodplains, improves emission inventories via system-specific emission factors and highlights climate impacts on river-floodplain GHG emissions.