This study intended to compare physical and chemical variables, net ecosystem metabolism (production – respiration) and calcification-carbonate dissolution rates in two coastal reefs subject to different levels of anthropogenic inputs of nutrients and organic matter. The coast surrounding Coroa Vermelha reef presented a higher degree of urbanization and touristic activities than Taipus de Fora at the time of sampling. The temperature, dissolved inorganic nutrients, total alkalinity, and total suspended solids were significantly higher in Coroa Vermelha reef, probably as a result of the anthropogenic inputs. These variables in Taipus de Fora were comparable to those found in the literature for Recife de Fora, an offshore protected reef and other less impacted reefs.  Total alkalinity, dissolved inorganic carbon and carbon dioxide partial pressure were lower and pH was higher in the reef flat than at the surrounding seawater. There was a prevalence of an influx of atmospheric carbon dioxide to reef water, net autotrophy and calcification. A significant correlation was observed between net calcification and net community metabolism. The benthic photosynthesis in the reef flat during low tide decreases the carbon dioxide partial pressure and increases the aragonite saturation state, establishing thermodynamic conditions that favor calcification.