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

Abstract Natural river-floodplains are significant sources of greenhouse gases (GHG) including CO 2 and CH 4 , yet the role of hydrological connectivity in shaping aquatic fluxes of these gases ( F CO 2 and F CH 4 ) remains unclear. This study was conducted in a temperate river-floodplain system (Poland), using manual and automated flux chambers where we measured 1776 F CH 4 and 1783 F CO 2 during various water levels in 15 locations across dormant and growing seasons. The system showed a high spatio-temporal variability, with the highest F CH 4 in the disconnected sidearms and the highest F CO₂ in the river. Hydrology strongly regulated F CO 2 , while F CH 4 responses were jointly shaped by temperature, connectivity and local hydrological conditions. The system was the strongest source of GHGs (in CO 2 -equivalent; CO 2-eq ) in the summer and the weakest in the spring. Over the last ten years (2015–2025), significantly more of the CO 2-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 F CO 2 and F CH 4 in natural river-floodplains, improves emission inventories via system-specific emission factors and highlights climate impacts on river-floodplain GHG emissions.