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A one-dimensional (1-D) model for an enclosed basin (lake) is presented, which reproduces temperature, horizontal velocities, oxygen, carbon dioxide and methane in the basin. All prognostic variables are treated in a unified manner via a generic 1-D transport equation for horizontally averaged property. A water body interacts with underlying sediments. These sediments are represented by a set of vertical columns with heat, moisture and CH₄ transport inside. The model is validated vs. a comprehensive observational data set gathered at Kuivajärvi Lake (southern Finland), demonstrating a fair agreement. The value of a key calibration constant, regulating the magnitude of methane production in sediments, corresponded well to that obtained from another two lakes. We demonstrated via surface seiche parameterization that the near-bottom turbulence induced by surface seiches is likely to significantly affect CH₄ accumulation there. Furthermore, our results suggest that a gas transfer through thermocline under intense internal seiche motions is a bottleneck in quantifying greenhouse gas dynamics in dimictic lakes, which calls for further research.