AbstractThe inner shelf waters off Southeastern Brazil are periodically enriched by bottom intrusions of the cold and nutrient‐rich South Atlantic Central Water (SACW), which is transported offshore by the Brazil Current. This study examined the temporal contrasts in abundance and structure of pelagic copepod assemblages in a neritic station off Ubatuba, in relation to hydrography and phytoplankton biomass, to investigate the effects of SACW bottom intrusions on copepod population dynamics during three consecutive years. The water‐column characteristics shifted from a well‐mixed, more turbid and phytoplankton‐poor scenario during subsidence conditions to a stratified, less turbid and high Chl‐a concentration scenario during SACW bottom intrusions, leading to increased copepod diversity, abundance, and biomass. The rise in copepod diversity during SACW intrusions was related to the contribution of oceanic species in addition to coastal water species. The copepod community was numerically dominated by small‐sized species, such as Oncaea waldemari, Oithona plumifera, and clausocalanid and paracalanid copepodids, regardless of seasonality and SACW intrusions. Some large calanoid species contributed considerably to the total copepod biomass during intrusions. In addition to confirming that SACW seasonal intrusions play a key role in pelagic processes off Southeast Brazil, this study showed that the multiannual variability of SACW seasonal intrusions is important in regulating the structure and dynamics of copepod communities in this subtropical area.