In this study, we examined the relationship between sea surface temperature (SST) and phytoplankton abundance in coastal regions of the Brazilian South Atlantic: São Paulo, Paraná, and Santa Catarina, and the Protection Area of Southern right whales (Eubalaena australis) in Santa Catarina (APA), a conservation zone established along 130 km of coastline. Using SST and chlorophyll‐a (Chl‐a) data from 2002 to 2023, we found significant differences in SST between the regions, with São Paulo having the highest SST, followed by Paraná and Santa Catarina. All locations showed a consistent increase in SST over the years, with North Santa Catarina, APA and São Paulo experiencing the lowest rate of increase. Correlation analyses between SST and Chl‐a revealed a stronger inverse relationship in North Santa Catarina and APA, indicating an increased response of Chl‐a to SST variations in this region. The presence of protected area appears to play an essential role in reducing the negative impacts of increasing SST. Specifically, while there is a wealth of research on the consequences of global warming on diverse coastal and oceanic areas, heterogeneity among different settings persists and the causes for this necessitating attention. Our findings have implications for both localized scientific approaches and broader climate policies, emphasizing the importance of considering coastal ecosystem resilience to climate change in future conservation and adaptation strategies.