We monitored the Black Tern (Chlidonias niger) population at Agency and Upper Klamath Lakes, in the Klamath Basin, Oregon, from 2001–2010. We estimated that the population of adult Black Terns declined at these 2 joined waterbodies by 8.4% annually. In contrast, our analysis of Breeding Bird Survey data for the Bird Conservation Region 9/Great Basin during the same period did not detect a trend. Knowledge of local short-term trends in the Klamath Basin can contribute to understanding regional and continental population declines of this species. Water levels, which may affect both habitat availability and suitability, were relatively stable from 2001–2009, but dropped in 2010 and remained depressed from 2010–2014. The direct effect of water-level fluctuations on habitat availability (hectares of habitat loss) is not well understood. Water allocation is a management challenge in this region and has been exacerbated by recent drought conditions. In combination, understanding trends and causal factors can inform water management, restoration, and habitat protection, all of which may contribute to reversing the decline of breeding terns.