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Abstract The Monin‐Obukhov Similarity Theory (MOST) links turbulent statistics to surface fluxes through universal functions. Here, we investigate its performance over a large lake, where none of its assumptions (flat homogeneous surface) are obviously violated. We probe the connection between the variance budget terms and departure from the nondimensional flux‐variance function for CO₂, water vapor, and temperature. Our results indicate that both the variance storage and its vertical transport affect MOST, and these terms are most significant when small fluxes and near neutral conditions were prevalent. Such conditions are common over lakes and oceans, especially for CO₂, underlining the limitation of using any MOST‐based methods to compute small fluxes. We further show that the relaxed eddy accumulation (REA) method is more robust and less sensitive to storage and transport, adequately reproducing the eddy‐covariance fluxes even for the smallest flux magnitudes. Therefore, we recommend REA over MOST methods for trace‐gas flux estimation.