Intertidal mudflats are an important component of the coastal geomorphological system at the interface between ocean and land. Accurate and up-to-date mapping of intertidal topography at high spatial resolution, and tracking of its changes over time, are essential for coastal habitat protection, sustainable management and vulnerability analysis. Compared with ground-based or airborne terrain mapping, the satellite-based waterline method is more cost-effective for constructing large-scale intertidal topography. However, the accuracy of the waterline method is affected by the extraction of waterlines and the calibration of waterline height. The blurred boundary between turbid water and mudflats in the tide-dominated estuary brings enormous challenges in accurate waterline extraction, and the errors in estuarine water level simulations prevent the direct calibration of waterline heights. To address these issues, this paper developed a novel deep learning method using a parallel self-attention mechanism and boundary-focused hybrid loss to extract turbid estuarine waterlines accurately from dense Sentinel-2 time series. UAV photogrammetric surveys were employed to calibrate waterline heights rather than the simulated water levels, such that the error propagation is constrained effectively. Annual intertidal topographic maps of the Yangtze estuary in China were generated from 2020 to 2022 using the optimized waterline method. Experimental results demonstrate that the proposed deep learning method could achieve excellent performance in land and water segmentation in time-varying tidal environments, with better generalization capability compared with benchmark U-Net, U-Net++ and U-Net+++ models. The comparison between the generated topography and UAV photogrammetric observations resulted in an RMSE of 13 cm, indicating the effectiveness of the optimized waterline method in monitoring morphological changes in estuarine mudflats. The generated topographic maps successfully identified hotspots of mudflat erosion and deposition. Specifically, the mudflats connected to the land predominantly experienced deposition of 10–20 cm over the two-year period, whereas the offshore sandbars exhibited instability and significant erosion of 20–60 cm during the same period. These topographic maps serve as valuable datasets for providing scientific baseline information to support coastal management decisions.