Drowned coral reefs on rapidly subsiding margins possess a unique archive of sea level and climate changes, generally unavailable from stable or uplifting margins. Using available field observations and sedimentary, radiometric age, and numerical modeling data, we propose a new model of submerged reef development around Hawaii during the last two glacial cycles (250 kyr). This model provides a quantitative predictive stratigraphy for the reefs that we argue, if drilled, will yield new information on sea level and climate changes, as well as coral reef response over the last 250 kyr. Comparing the observational and numerical modeling data, combined with sensitivity testing, we present our “best case” scenario for the evolution of the drowned lowstand reefs now at −400 (H2) and −150 m (H1). We find that growth rates of 2.5–2.85 m/kyr for the main shallow reef building facies, a subsidence rate of 2.5 m/kyr, and a variable basement substrate configuration best explain the observational data. Modeling of the internal stratigraphic succession of the reefs shows that the number and thickness of shallow reef units, as well as the frequency and duration of subaerial exposure and reef-drowning events, are sensitive to the frequency and amplitude of eustatic sea level variations but not the rate of subaerial erosion. H2 and H1 initiated growth during stable eustatic sea level conditions during highstands circa 222 ka (MIS7) and circa 126 ka (MIS5e), respectively. Both H2 and H1 have a long and complex growth history, growing episodically for ∼90 kyr. Precessional (∼20 kyr) and higher-frequency, suborbital eustatic sea level fluctuations dominate, with each reef experiencing repeated but brief (<5–10 kyr) drowning and subaerial exposure, producing a complex layer cake stratigraphy of shallow (0–30 m) coral reef units separated by either subaerial exposure horizons or thin, intermediate (30–60 m) coralgal units. Final drowning of H2 and H1 occurs during the penultimate (133–134 ka) and last deglaciation (12–14 ka). These findings are consistent with available age data and qualitative predictions of previous studies around Hawaii.