Climate projections of ocean variables are essential to inform adaptation strategies and plans involving open and coastal oceanic regions. Assessment of baseline and projections of sea surface temperature (SST), pH, dissolved oxygen (DO), mean sea level (MSL), waves coastal flooding within Ecuador’s Exclusive Economic Zone, including Galapagos Islands are reported herein. With different magnitudes of change, both near-future (2021–2050) and far-future projections (2051–2080) show a statistically robust increase in SST, MSL rise and a reduction in pH, a proxy for acidification. In contrast, DO decrease is only observed in surface (0–100 m) but not in subsurface waters (100–400 m). The likelihood of extreme sea level events in the coastal cities of La Libertad, Manta and Esmeraldas would remain almost unchanged for near-future projections (2026–2045) whereas, for end-of-century projections (2081–2100), historical 1 in a 100-year extreme flooding events would become yearly occurrences. The generated data product offers a state-of-the-art research and management tool for the 21st century under the combined stressors of global climate change. Since the eastern Tropical Pacific Ocean is one of the most productive and biodiverse worldwide due to the equatorial upwelling system, possible impacts on marine biodiversity, social, and economic systems are discussed.