The Congo Basin, home to the world’s second-largest tropical rainforest, is a biodiversity hotspot and a critical carbon sink. Its varied habitats—including rainforests, savannas, miombo woodlands, freshwater systems, peatlands, and coastal mangroves—support essential ecosystem functions. The Cuvette Centrale peatlands alone store an estimated 30 gigatons of carbon, underscoring the Basin’s climate significance. This review examines climate change impacts on the Basin’s ecosystems, focusing on ecological processes, carbon dynamics, and species responses. The region is increasingly vulnerable to climate change and human pressures. Temperatures are rising faster than the global average, projected to increase 1.5–2 °C by century’s end, while rainfall is becoming more erratic, driving longer dry seasons, flash droughts, and altered flood cycles. These changes, combined with deforestation and land-use conversion, disrupt ecosystem processes. Forests show shift in phenological cycles affecting frugivores and herbivores; savannas face woody encroachment under rising CO₂; freshwater systems experience reduced water quality and declining fish populations; peatlands risk carbon release from lowered water tables; and mangroves are threatened by sea-level rise and reduced freshwater inflows. These ecological shifts have cascading effects, altering carbon and water cycles, nutrient dynamics, and species interactions. Changes in evapotranspiration and rainfall recycling further influence global climate patterns, including the Intertropical Convergence Zone, highlighting the Basin’s role in Earth system regulation. Maintaining the Congo Basin’s ecological integrity is critical for regional resilience and global climate mitigation. Integrated research, targeted conservation, and sustainable land-use practices are urgently needed to safeguard these ecosystems against intensifying climatic and anthropogenic pressures.