Primary producers rarely exist under their ideal conditions, with key processes often limited by resource availability. As human activities modify environmental conditions, and therefore resource availability, some species may be released from these limitations while others are not, potentially disrupting community structure. In order to examine the limitations experienced by algal functional groups that characterise alternate community structures (i.e. turf-forming algae and canopy-forming kelp), we exposed these groups to contemporary and enriched levels of carbon dioxide (CO2) and nutrients. Turfs responded to the individual enrichment of both CO2 and nutrients, with the greatest shift in the biomass and carbon:nitrogen (C:N) ratios observed under their combined enrichment. In contrast, kelp responded to enriched nutrients, but not enriched CO2. We hypothesise that the differing limitations reflect the contrasting physiologies of these functional groups, specifically their methods of C acquisition, such as the possession and/or efficiency of a carbon concentrating mechanism (CCM). Importantly, our results reveal that these functional groups, whose interactions structure entire communities, experience distinct resource limitations, with some potentially limited by a single type of resource (i.e. kelp by nutrients), while others may be co-limited (i.e. turf by CO2 and nutrients). Consequently, the identification of how alternate conditions modify resource availability and limitations may facilitate anticipation of the future sustainability of major ecosystem components and the communities they support.