Detailed surveys of the upper Hudson River Estuary and its floodplain from the early 1900s and digital mapping of the same areas today provide an opportunity to evaluate changes over the 20th century. This study uses a geographic information system to quantitatively compare water areas and islands mapped by the United States Army Corps of Engineers in 1907 and 1911 along an approximately 60-km reach from Athens to Troy, NY, with the same features mapped in the late 20th century. The comparison shows a substantial decrease in total water area approximately 30% less than the 1907–1911 quantity, with secondary channels disproportionally affected (~70% less). The number and total area of islands has also dramatically decreased by approximately 65% and 85%, respectively. These changes primarily reflect the success of navigation improvement projects undertaken since the 19th century that transformed a shallow, island-braided river in the study reach to one characterized by a deeper, single-thread channel. Dredge spoils from the main channel were used to fill secondary channels and other backwater areas, a practice with implications for reproduction, growth and/or survival of native plants and animals. Published in 2011 by John Wiley & Sons, Ltd.