Windthrow is a major forest disturbance source in Europe. The impact of management (salvage logging) and no-management (deadwood left in ecosystem) treatments on carbon and water fluxes of Norway spruce stand affected by windthrow were analysed. The net ecosystem production (NEP), gross primary production (GPP), ecosystem respiration (R_eco) and evapotranspiration (ET) were measured with eddy-covariance tower during 2019–2022 period. Additional chamber gas-exchange measurements, and vegetation inventory were performed. The unmanaged site had greater vegetation diversity and plant abundance, with higher leaf area index (LAI). The managed site showed overall higher NEP, lower GPP, lower R_eco, lower GPP based water-use efficiency (WUE_GPP), but higher NEP based WUE_NEP, compared with unmanaged site. The ET showed no clear trend between the two treatments. The higher GPP of unmanaged site can be linked to greater abundance of herbaceous species, which showed significantly higher photosynthetic capacity than the tree species. Moreover, the higher WUE_GPP of unmanaged site can be affected also by the higher LAI of the unmanaged site. Nevertheless, if the R_eco is accounted for in WUE_NEP, the differences between sites are reversed and the unmanaged site had lower WUE_NEP compared to the managed site. The option to leave the disturbed site without management leads to more productive ecosystem (GPP), with greater species diversity and abundance, but also with greater R_eco and lower WUE_NEP. The discrepancy between WUE_GPP and WUE_NEP suggests that studies analysing natural ecosystems affected by disturbances should use WUE_NEP to account for R_eco carbon losses and avoid mis-interpreting the ecosystem carbon-water balance with WUE_GPP.