Physics-based hydrodynamic models are essential for accurate flood prediction but are computationally expensive, limiting their applicability for real-time forecasting and probabilistic analyses. Conversely, pure machine learning (ML) models offer both computational efficiency and accuracy but often lack interpretability. To address this gap, we propose SGUnet, a physics-informed ML model and a hybrid theory-guided data science approach, for rapid, high-resolution flood mapping. It utilizes a neural network with U-Net architecture and integrates subgrid-based coarse-grid hydrodynamic model predictions as initial estimates, upskilling them to achieve fine-grid model accuracy. Unlike traditional hydrodynamic models, the subgrid method embeds fine-scale topographic details within coarse-grid cells, enhancing both computational efficiency and predictive accuracy. SGUnet processes flood depth raster patches (512 × 512 pixels) and corresponding digital elevation models as inputs. It functions as a deep learning-based corrector, refining flood predictions from numerical simulators. Trained through supervised learning, SGUnet learns to correct deviations in coarse-grid predictions using fine-grid model outputs as target values. The model is evaluated across three large Australian watersheds—Wollombi, Chowilla, and Burnett River—using HEC-RAS flood simulations with subgrid formulation. SGUnet reduces root mean squared error by a factor of 4.5–5.3 compared to coarse-grid models, achieves a critical success index exceeding 0.9 for flood extent mapping, and delivers a 50x speed-up over fine-grid hydrodynamic models. Furthermore, SGUnet outperforms a state-of-the-art ML-based upskilling model in depth and extent predictions. By effectively correcting flood artifacts from coarse-grid models, SGUnet achieves near fine-grid accuracy with significantly reduced computational cost, demonstrating its potential for real-time flood risk assessment.