Estuaries are locally and globally critical ecosystems, many of which are undergoing major transformations in response to climate change and other anthropogenic stresses. Understanding estuarine ecosystems and the changes they are experiencing requires foundational knowledge of circulation and sediment dynamics. Here we use high-resolution simulations from an unstructured grid circulation model, skill-assessed against a robust data set from the Columbia River estuary, to characterize circulation, sediment dynamics and the dominant pathways through the system. We then use these characterizations to develop a new three-dimensional conceptual model of prevailing sediment dynamics and obtain novel insights into the sources and dynamics of ecologically critical estuarine turbidity maxima. Finally, we use a combination of observations and numerical simulations to develop system-wide estimates of light availability and bacterial productivity based on suspended sediment concentrations.