The fluvial to marine transition zone (FMTZ) is a dynamic environment, subject to a mixture of marine and riverine forcing mechanisms. These processes control deposition of sediments, which can hold valuable natural resources. However, due to the complex process regime, the sedimentary successions from these areas can be difficult to interpret. This study aims to improve depositional models by linking quantified measurements of the active processes to their deposits along the transition zone, using a modern example of these systems, the Waihou River in the North Island of Aotearoa-New Zealand. This study produced three main findings, which are relevant to people researching ancient shallow marine strata: 1) The locus of mud deposition occurs in the middle of the transition zone due the combined influence of depositional and preservational controls. Mixing of marine and freshwater reduces landward, which limits flocculation, and hence, deposition of mud upstream. In contrast, preservation of mud deposits is reduced towards the mouth of the river as a result of faster flow speeds. Midway between these two endpoints is a region where deposition and preservation of mud is the largest within the FMTZ. 2) Fluid mud deposits are poorly preserved in the deepest parts of channels, likely due to the high energy levels in this environment. Nevertheless, our results do not preclude the possibility that significant accumulations may occur in the shallow parts of the cross-channel profile. 3) Mud facies diversity is an indicator of depositional position along the FMTZ. Facies diversity was greatest at the middle observational site, which corresponds to the area that is subject to the most variable process regime. The landward and seaward ends of the transition zone exhibit a greater level of dominance in solely riverine or marine depositional processes, respectively. This study yields new insights into the process-response relationships for mud deposition at the interface of land to sea.