In tidally dominated deltas, sediment discharged from the river sources must transit through an estuarine region located within the distributary channels, where particle pathways can undergo significant transformations. Water column profiles and time series data were collected in the distributaries and shallow nearshore region offshore of the Fly River, Papua New Guinea, during monsoon conditions of 2003 and 2004. Within the distributaries of this tidally dominated delta, near-bed fluid mud concentrations were observed at the estuarine turbidity maximum. Discharge and morphology of the distributaries determine the location of estuarine processes and control the sediment flux to the marine environment. Sediment delivery from the delta to the broad shallow nearshore region northeast of the river mouth and to the steep Umuda shelf valley is influenced by the shorter pathway of the northernmost distributary. The shallowest portion of the nearshore region (<10 m water depth) is a zone of temporary storage where unconsolidated sediment is easily resuspended. Umuda shelf valley constrains and enhances tidal currents and provides a steep conduit to seaward transport of fluid muds. Comparison of 2003 and 2004 data shows evidence of reduction in freshwater supply to the Gulf of Papua during the moderate 2003 El Niño conditions. El Niño creates a large negative perturbation (i.e., low flow) to the relatively constant sediment discharge. This reduction of discharge limits transport of sediment from the distributaries to the nearshore zone of temporary storage. As the sediment stored near shore feeds the prograding clinoform found seaward, the perturbation propagates throughout the dispersal system.