Previous interdisciplinary paleoenvironmental and archaeological research along the Río Verde Valley of Oaxaca, Mexico, showed that Holocene erosion in the highland valleys of the upper drainage basin triggered geomorphic changes in the river's coastal floodplain. This article uses stratigraphic data from sediment cores extracted from Laguna Pastoría, an estuary in the lower Río Verde Valley, to examine changes in coastal geomorphology potentially triggered by highland erosion. Coastal lagoon sediments contain a stratigraphically and chronologically distinct record of major hurricane strikes during late Holocene times. Three distinct storm facies are identified from sediment cores obtained from Laguna Pastoría, which indicate that profound coastal environmental changes occurred within the region and are correlated with increased sediment supplied from highland erosion. The Chione/Laevicardium facies was deposited in an open bay while the Mytella/barnacle facies and sand facies were deposited in an enclosed lagoon following bay barrier formation. We argue that highland erosion triggered major geomorphic changes in the lowlands including bay barrier formation by ∼2500 cal yr B.P. These environmental changes may have had significant effects on human populations in the region. The lagoon stratigraphy further indicates an increase in mid–late Holocene hurricane activity, possibly caused by increased El Niño frequencies.