The impact of invasive species on recipient communities can vary with environmental context and across levels of biological complexity. We investigated how an established invasive seaweed species affected the biomass, eco-physiology, carbon and nitrogen storage capacity of native seaweeds at sites with a different environmental setting due to a persistent upwelling in northern Spain. We removed the invasive Japanese wireweed Sargassum muticum from intertidal rock pools once every month during a one-year period and used an in-situ stable isotope pulse-chase labeling to estimate gross primary production (GPP), nitrogen uptake rate, 13C-carbon and 15N-nitrogen storage capacities. Following the addition of 13C-enriched bicarbonate and 15N-enriched nitrate to the seawater in the rock pools during the period of the low tide, we sampled macroalgal thalli at incoming tide to determine label uptake rate. After four days, we sampled macroalgal assemblages to determine both label storage capacity and biomass. After one year of removal there was no change in the macroalgal assemblage. However, both the GPP and 13C-carbon storage capacity were higher in the turf-forming Corallina spp. and, sometimes, in the canopy-forming Bifurcaria bifurcata. Nitrogen uptake rate followed similar, but more variable results. Although S. muticum inhibited carbon storage capacity of native species, the assemblage-level 13C-carbon storage was similar in the S. muticum-removed and control rock pools because the presence of the invasive species compensated for the functional loss of native species, particularly at sites where it was most abundant. No obvious effects were observed in relation to the environmental setting. Overall, the effect of the invasive S. muticum on carbon flow appeared to be mediated both by the effects on resource-use efficiency of native species and by its own biomass. Integrating physiological and assemblage-level responses can provide a broad understanding of how invasive species affect recipient communities and ecosystem functioning.