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<p>Freshwaters are important emitters of carbon dioxide (<span class="inline-formula">CO₂</span>) and methane (<span class="inline-formula">CH₄</span>), two potent greenhouse gases (GHGs). While aquatic surface GHG fluxes have been extensively measured, there is much less information about their underlying sources. In lakes and reservoirs, surface GHG can originate from horizontal riverine flow, the hypolimnion, littoral sediments, and water column metabolism. These sources are generally studied separately, leading to a fragmented assessment of their relative role in sustaining <span class="inline-formula">CO₂</span> and <span class="inline-formula">CH₄</span> surface fluxes. In this study, we quantified sources and sinks of <span class="inline-formula">CO₂</span> and <span class="inline-formula">CH₄</span> in the epilimnion along a hydrological continuum in a permanently stratified tropical reservoir (Borneo). Results showed that horizontal inputs are an important source of both <span class="inline-formula">CO₂</span> and <span class="inline-formula">CH₄</span> (<span class="inline-formula">&gt;90</span> % of surface emissions) in the upstream reservoir branches. However, this contribution fades along the hydrological continuum, becoming negligible in the main basin of the reservoir, where <span class="inline-formula">CO₂</span> and <span class="inline-formula">CH₄</span> are uncoupled and driven by different processes. In the main basin, vertical <span class="inline-formula">CO₂</span> inputs and sediment <span class="inline-formula">CH₄</span> inputs contributed to on average 60 <span class="inline-formula">%</span> and 23 <span class="inline-formula">%</span> respectively to the surface fluxes of the corresponding gas. Water column metabolism exhibited wide amplitude and range for both gases, making it a highly variable component, but with a large potential to influence surface GHG budgets in either direction. Overall our results show that sources sustaining surface <span class="inline-formula">CO₂</span> and <span class="inline-formula">CH₄</span> fluxes vary spatially and between the two gases, with internal metabolism acting as a fluctuating but key modulator. However, this study also highlights challenges and knowledge gaps related to estimating ecosystem-scale <span class="inline-formula">CO₂</span> and <span class="inline-formula">CH₄</span> metabolism, which hinder aquatic GHG flux predictions.</p>