Living coastal barriers, such as coral reefs, tidal marshes, mangroves and shellfish beds are widely recognized for their potential role in mitigating flood risk. Limited data exists, however, for assessing the effectiveness of these natural defenses as forms of flood mitigation. In particular, very few mature shellfish beds exist today for modern study due to their destruction in the past few centuries. As an alternative method of study, we present here sedimentary reconstructions of storm overwash from coastal ponds internal to New York Harbor. We use these reconstructions to show that the initial degradation of oyster beds following European settlement of the area coincides with a significant increase in wave-derived overwash deposition at all three of our field sites. Numerical simulations of two flood events of record in the harbor (Hurricane Sandy and a severe winter storm in 1992) were run without and with oyster beds of varying heights (1 m above the seafloor-to-intertidal). Simulations show that the removal of these oyster beds increases wave energy directly off-shore of our field sites by between 30% and 200%. Sedimentary reconstructions and wave modeling experiments therefore both support oyster beds serving as a significant form of coastal protection prior to European disturbance. Copyright © 2016 John Wiley & Sons, Ltd.