The Loxahatchee River, a 500 km² watershed on the southeast Florida coast, is a barrier-impounded drowned river valley experiencing rapid urbanization during the past 50 years. The estuary is currently composed of a sandy central basin with bifurcating forks accumulating organic-rich muddy sands. The Northwest Fork drains natural forest, residential, and agricultural catchments and has a much larger bayhead delta than the channelized Southwest Fork, which is only 50 years old and diverts much of the flow from the Northwest Fork. Sediment accumulation rates within muddy sand deposits are about 2–3 mm a⁻¹, commensurate within error of the current rate of local sea-level rise. Previously established Holocene accumulation rates are close to relative sea-level rise, implying that sediment accumulation is in equilibrium with the creation of accommodation space. The main anthropogenic influences have been changes in surface sediment texture corresponding to dredging-induced modification of tidal currents and a localized >threefold increase in sediment accumulation rate supplied by sources local to the estuary. Late Holocene sedimentation has been episodic, and lithofacies vary from bioturbated transgressive sands at depth to peat and laminated fine-grained sediments then back to mottled muddy sands in the uppermost strata. This facies transition is attributed to a change of water column stratification conditions caused by decreased tidal flushing in the estuary possibly brought about by variation in sea level or episodic inlet closure by littoral sand transport. The magnitude of the anthropogenic changes in sedimentation is roughly equal with natural changes in lithofacies formation.