Eddy covariance (EC) data are vital for studying carbon and water fluxes but often mask species-specific responses in mixed forests. At a Black Forest site with beech and Douglas fir, we combined EC data with ecosystem modeling to separate species contributions. Results show EC fluxes reflect species abundance within flux footprints, though responses vary seasonally. Accounting for these differences is key for gap-filling, accurate budgets, and understanding mixed forests’ climate resilience.