<p>Although reef systems are facing increasing threats from anthropogenic impacts worldwide, such as overfishing and climate change, baseline-based assessments remain scarce in the Southwestern Atlantic. Here, our objectives were: (i) to assess changes in the rocky reef fish and benthic assemblages two decades after the first assessment (2001 and 2023 baselines), and (ii) to evaluate their current overlap along the Guarapari coast, eastern Brazil. Surveys were conducted in the no-take zone of Três Ilhas (TRE), and two unprotected islands, Escalvada (ESC) and Rasas (RAS). Current data collection involved 424 underwater visual censuses and 108 photoquadrats. Substantial changes in fish abundance were observed when comparing data from 69 species between both baselines. At TRE, 27 species showed significant changes in abundance, with 19 experiencing declines, while at ESC, 38 species exhibited significant changes, including 31 declines. A notable shift in fish trophic groups was recorded, with a general increase in roving herbivorous and sessile invertebrate feeders alongside a decline in omnivorous, mobile invertivorous feeders, and carnivores. We reported a sharp reduction in the coverage of massive corals and milleporids at the TRE. Conversely, groups such as octocorals, sponges, and zoanthids experienced significant declines on both islands. Current differences between islands include higher size and abundance of commercially targeted fish, such as snappers, haemulids, and labrids, as well, higher assemblage diversity at greater distances from the coast. In conclusion, despite not having constant monitoring, baseline assessments could be valuable for identifying changes in biotic assemblages, assisting conservation efforts, and management strategies.</p>