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Salt intrusion poses a global threat to estuaries and deltas, exacerbated by climate change, drought, and sea level rise. This observational study investigates the impact of river discharge, wind, and tidal variations on salt intrusion in a branching river delta during drought. The complexity and spatial extent of deltas make comprehensive measurements challenging and rare. In this paper, we present a 17‐week data set of a historic drought in the Rhine‐Meuse Delta, capturing dynamics in a multiple‐channel system in a wide range of conditions. Key characteristics of this low‐lying delta are its branching channel network and complicated, human‐controlled discharge. Despite the system's complexity, we found that the subtidal salt intrusion length, defined by the 2 PSU isohaline , follows a power law relationship with Rhine River discharge . Subtidal water level variations contribute to short‐term variations in intrusion length, shifting the limit of salt intrusion upstream and downstream with a distance similar to the tidal excursion length. This can be attributed to the up‐estuary transport of seawater, caused by the estuary adjusting to variations in water levels at its mouth. However, spring‐neap variation in the tidal range does not alter the subtidal salt intrusion length. Side branches exhibit distinct dynamics from the main river, and their most important control is the downstream salinity. We show that treating the side branches separately is crucial to incorporate the highly variable downstream boundary condition, and may apply in other deltas or complex estuaries.