The Trinity River and the sediments that infill its incised valley system are well-constrained in terms of time and space properties of the sediment deposits and resulting stratigraphy. The Trinity River is an excellent natural laboratory to test fluvial morphodynamic concepts that could be used to examine the processes of incised valley infill. We develop a numerical model that links sediment transport processes and the production of stratigraphy to evaluate the effects of Holocene transgression on the development of Trinity stratigraphy. We simulate the mechanics of channel fill and avulsions for the Trinity River, by coupling fluid flow, sediment transport and channel response, constrained by modern and early Holocene conditions. Our results show how non-uniform flow produces loci of sediment deposition, which backstep within the channel as base-level rises, and coincide with the avulsion locations. There is an upstream retreat as the rate of base-level rise increases (transgression). Additionally, we show how including a floodplain parameter within the model framework influences the calculated time for avulsion by changing the amount of sediment deposited within the channel. Our model is applied over century to millennial timescales, and is utilized to evaluate basin scale patterns of known stratigraphic variability. Because the model is well-constrained, our results have application for predicting stratigraphy for other fluvial-deltaic systems undergoing transgression. This is especially important for predicting the valley infill of systems that lack the robust constraint exhibited by the Trinity incised valley system.