Over the past 50 years, the population of Continental Black-tailed Godwits Limosa limosa limosa breeding of the East Atlantic Flyway has been in steep decline. This decline has previously been documented in trend analyses and six Netherlands-wide count-based population estimates, the last of which was completed in 1999. We provide an updated population size estimate and describe inter-annual fluctuations in the population between 2007 and 2015. To generate these estimates, we integrated a mark-recapture survival analysis with estimates of the densities of colour-marked individuals at migratory staging sites with known proportions of Continental and Icelandic L. l. islandica Black-tailed Godwits within a Bayesian framework. The use of these analytical techniques means that, in contrast with earlier efforts, our estimates are accompanied with confidence intervals, allowing us to estimate the population size with known precision. Using additional information on the breeding destination of 43 godwits equipped with satellite transmitters at Iberian staging areas, we found that 87% (75–95% 95% CI) of the nominate subspecies in the East Atlantic Flyway breed in The Netherlands. We estimated that the number of breeding pairs in The Netherlands has declined from 47,000 (38,000–56,000) pairs in 2007 to 33,000 (26,000–41,000) in 2015. Despite a temporary increase in 2010 and 2011, the population declined by an average of 3.7% per year over the entire period from 2007–2015, and by 6.3% from 2011–2015. We conclude that investing in an intensive demographic programme at a regional scale, when combined with targeted resightings of marked individuals elsewhere, can yield population estimates at the flyway scale.