Abstract. Freshwaters are important emitters of carbon dioxide (CO2) and
methane (CH4), 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 CO2 and CH4 surface fluxes. In this study, we
quantified sources and sinks of CO2 and CH4 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 CO2 and CH4 (>90 % 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 CO2 and CH4 are
uncoupled and driven by different processes. In the main basin, vertical
CO2 inputs and sediment CH4 inputs contributed to on
average 60 % and 23 % 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 CO2 and CH4
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
CO2 and CH4 metabolism, which hinder aquatic GHG flux
predictions.