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Climate change will lead to community shifts and increase the vulnerability of coastal marine ecosystems, but there is yet insufficient detail of how early life stages of marine populations are linked to oceanic-climate dynamics. This study aimed to investigate how ocean-climate variability is associated with spatial and temporal changes in benthic larval recruitment of tropical reef assemblages. Recruitment (abundance, richness, and diversity) of benthic invertebrates was monitored for one year on macroalgal beds in four rocky reefs in a marine protected region in the Eastern coast of Brazil, and compared to fluctuations in meteo-oceanographic conditions at multiple temporal scales (days, weeks, and months). Our results revealed that recruitment of benthic invertebrates varies widely (up to 15 orders of magnitude) among sampled reefs and in time, with wave height, wind speed, and sea temperature being significantly related to recruitment variability. We detected strong taxonomic variability in recruitment success and ocean-climate variables, which highlights the complexity of estimating community vulnerability to climate change in benthic communities. Given that macroalgal beds are key to recruitment of some species regionally (4-30 km), the protection of coastal nursery habitats may be critical for marine conservation and species adaptation in a climate change scenario. Considering the projected ocean-climate change in IPCC scenarios, our study suggests that recruitment of marine populations in coastal reefs could be highly sensitive to climate change in the tropical South Atlantic Ocean.