Knowing the abundance of a population is a crucial component to assess its conservation status and develop effective conservation plans. For most cetaceans, abundance estimation is difficult given their cryptic and mobile nature, especially when the population is small and has a transnational distribution. In the Baltic Sea, the number of harbour porpoises (Phocoena phocoena) has collapsed since the mid-20^th century and the Baltic Proper harbour porpoise is listed as Critically Endangered by the IUCN and HELCOM; however, its abundance remains unknown. Here, one of the largest ever passive acoustic monitoring studies was carried out by eight Baltic Sea nations to estimate the abundance of the Baltic Proper harbour porpoise for the first time. By logging porpoise echolocation signals at 298 stations during May 2011-April 2013, calibrating the loggers’ spatial detection performance at sea, and measuring the click rate of tagged individuals, we estimated an abundance of 71-1,105 individuals (95% CI, point estimate 491) during May-October within the population’s proposed management border. The small abundance estimate strongly supports that the Baltic Proper harbour porpoise is facing an extremely high risk of extinction, and highlights the need for immediate and efficient conservation actions through international cooperation. It also provides a starting point in monitoring the trend of the population abundance to evaluate the effectiveness of management measures and determine its interactions with the larger neighbouring Belt Sea population. Further, we offer evidence that design-based passive acoustic monitoring can generate reliable estimates of the abundance of rare and cryptic animal populations across large spatial scales.

Four main datasets are provided, together with meta-data and processing code files.

1. SAMBAH main survey: passive acoustic monitoring data collected by CPOD click loggers in the Baltic Sea May 2011-April 2013.

2. Great Belt tracking experiment: detection/nondetection of acoustically tracked harbour porpoises May-June 2013 in Great Belt, Denmark.

3. Playback experiment: detection/nondetection of artificial clicks produced to estimate click detectability during the SAMBAH main survey and Great Belt tracking experiment.

4. Tagging study: click production and depth data from 6 tagged porpoises in Danish waters between May 2010 and April 2011.

See readme.txt file.