Low-lying, tropical, coral-reef-lined coastlines are becoming increasingly vulnerable to wave-driven flooding due to population growth, coral reef degradation, and sea-level rise. Early-warning systems (EWSs) are needed to enable coastal authorities to issue timely alerts and coordinate preparedness and evacuation measures for their coastal communities. At longer timescales, risk management and adaptation planning require robust assessments of future flooding hazard considering uncertainties. However, due to diversity in reef morphologies and complex reef hydrodynamics compared to sandy shorelines, there have been no robust analytical solutions for wave runup to allow for the development of large-scale coastal wave-driven flooding EWSs and risk assessment frameworks for reef-lined coasts. To address the need for fast, robust predictions of runup that account for the natural variability in coral reef morphologies, we constructed the BEWARE-2 (Broad-range Estimator of Wave Attack in Reef Environments) meta-process modeling system. We developed this meta-process model using a training dataset of hydrodynamics and wave runup computed by the XBeach Non-Hydrostatic process-based hydrodynamic model for 440 combinations of water level, wave height, and wave period with 195 representative reef profiles that encompass the natural diversity in real-world fringing coral reef systems. Through this innovation, BEWARE-2 can be applied in a larger range of coastal settings than meta-models that rely on a parametric description of the coral reef geometry. In the validation stage, the BEWARE-2 modeling system produced runup results that had a relative root mean square error of 13% and relative bias of 5% relative to runup simulated by XBeach Non-Hydrostatic for a large range of oceanographic forcing conditions and for diverse reef morphologies (root mean square error and bias 0.63 and 0.26 m, respectively, relative to mean simulated wave runup of 4.85 m). Incorporating parametric modifications in the modeling system to account for variations in reef roughness and beach slope allows for systematic errors (relative bias) in BEWARE-2 predictions to be reduced by a factor of 1.5–6.5 for relatively coarse or smooth reefs and mild or steep beach slopes. This prediction provided by the BEWARE-2 modeling system is faster by 4–5 orders of magnitude than the full, process-based hydrodynamic model and could therefore be integrated into large-scale EWSs for tropical, reef-lined coasts and used for large-scale flood risk assessments.