The Yangtze finless porpoise (Neophocaena asiaeorientalis asiaeorientalis), has experienced rapid declines in recent decades. We estimate its abundance based on surveys conducted between November and December 2017 in the main-stem of the Yangtze River and adjacent Poyang and Dongting Lakes. We compare these to published abundance estimates from 2006 and 2012, using a bootstrap resampling approach to make inference about population change over the 2006–2017 time period. Encounter rates of porpoise from additional surveys during this period provided another index for evaluating temporal changes in abundance in Poyang and Dongting Lakes. As of December 2017, free-ranging populations of this species are estimated at 1012 (95%CI: 791–1233) individuals of which 445 (95%CI: 295–595) occur in the main stem of the Yangtze River, 457 (95%CI: 329–634) in Poyang Lake, and 110 (95%CI: 65–187) in Dongting Lake. Porpoise numbers in main-stem of the Yangtze River and Dongting Lake declined rapidly from 2006 to 2012 (mean annual rates of −14% and −12%, respectively). These rates of decline greatly eased from 2012 to 2017 (−2.5% and +3% annual growth, respectively). In Poyang Lake, the encounter rates of porpoise have remained relatively stable between 2006 and 2017. This improved population trajectory was likely a joint consequence of government and public conservation efforts. However, fragmentation of porpoise populations in Yangtze River main-stem and significantly reduced migratory movements between the two adjoining lakes and the Yangtze main stem pose a continued threat to the long-term viability of this species. Further actions to improve habitat connectivity are urgently needed.