Sediments deposited from the Permian–Triassic boundary (~252 Ma) until the end-Smithian (Early Triassic; c. 250.7 Ma) in the Sonoma Foreland Basin show marked thickness variations between its southern (up to c. 250 m thick) and northern (up to c. 550 m thick) parts. This basin formed as a flexural response to the emplacement of the Golconda Allochthon during the Sonoma orogeny. Using a high-resolution backstripping approach, a numerical model and sediment thickness to obtain a quantitative subsidence analysis, we discuss the controlling factor(s) responsible for spatial variations in thickness. We show that sedimentary overload is not sufficient to explain the significant discrepancy observed in the sedimentary record of the basin. We argue that the inherited rheological properties of the basement terranes and spatial heterogeneity of the allochthon are of paramount importance in controlling the subsidence and thickness spatial distribution across the Sonoma Foreland Basin.