Coastal sediment budgets are a foundational source of information for coastal management decision-making. To quantify these budgets, coastal systems are often divided into “cells” based on jurisdictional boundaries or topography. However, such divisions do not account for the pathways that water and sediment particles actually take. In this study we quantify cell boundaries that emerge from numerical simulations of sand and water pathways in a barrier island-lagoon system in the Netherlands (the Western Wadden Sea). By quantifying Lagrangian particle pathways as a network, we can derive internally well-connected but externally disconnected modules. Here we show that large (O(10 km)) coherent modules develop from flow patterns at tidal timescales (12.5 h), and are persistent through varying tide and weather conditions. Conversely, modules derived from 100 µm sand pathways are less coherent and highly spatially fragmented. The difference in patterns likely relates to the longer timescales associated with sediment transport. These emergent patterns could be used to better inform coastal and estuarine management by providing physics-based sediment cell boundaries.