According to current experimental evidence, coral reefs could disappear within the century if CO2 emissions remain unabated. However, recent discoveries of diverse and high cover reefs that already live under extreme conditions suggest that some corals might thrive well under hot, high-pCO2, and deoxygenated seawater. Volcanic CO2 vents, semi-enclosed lagoons, and mangrove estuaries are unique study sites where one or more ecologically relevant parameters for life in the oceans are close to or even worse than currently projected for the year 2100. Although they do not perfectly mimic future conditions, these natural laboratories offer unique opportunities to explore the mechanisms that reef species could use to keep pace with climate change. To achieve this, it is essential to characterize their environment as a whole and accurately consider all possible environmental factors that may differ from what is expected in the future, possibly altering the ecosystem response. This study focuses on the semi-enclosed lagoon of Bouraké (New Caledonia, southwest Pacific Ocean) where a healthy reef ecosystem thrives in warm, acidified, and deoxygenated water. We used a multi-scale approach to characterize the main physical-chemical parameters and mapped the benthic community composition (i.e., corals, sponges, and macroalgae). The data revealed that most physical and chemical parameters are regulated by the tide, strongly fluctuate three to four times a day, and are entirely predictable. The seawater pH and dissolved oxygen decrease during falling tide and reach extreme low values at low tide (7.2 pHT and 1.9 mg O2 L−1 at Bouraké vs. 7.9 pHT and 5.5 mg O2 L−1 at reference reefs). Dissolved oxygen, temperature, and pH fluctuate according to the tide by up to 4.91 mg O2 L−1, 6.50 ∘C, and 0.69 pHT units on a single day. Furthermore, the concentration of most of the chemical parameters was 1 to 5 times higher at the Bouraké lagoon, particularly for organic and inorganic carbon and nitrogen but also for some nutrients, notably silicates. Surprisingly, despite extreme environmental conditions and altered seawater chemical composition measured at Bouraké, our results reveal a diverse and high cover community of macroalgae, sponges, and corals accounting for 28, 11, and 66 species, respectively. Both environmental variability and nutrient imbalance might contribute to their survival under such extreme environmental conditions. We describe the natural dynamics of the Bouraké ecosystem and its relevance as a natural laboratory to investigate the benthic organism's adaptive responses to multiple extreme environmental conditions.