The Marbled Murrelet (Brachyramphus marmoratus) is federally threatened in part of its range in western North America. Information on density and productivity is important for managing populations. Over an 18-yr period, we monitored murrelet density and productivity ratios during the breeding season along 170 km of shoreline of the San Juan Islands, Washington, USA. While murrelets occur throughout the coastal marine waters of Washington, the San Juan Islands support higher densities of murrelets during the breeding season than most other areas. From 1995 to 2012, the average density of adult murrelets declined significantly from 11.16 to 5.76 murrelets km⁻², a decline that mirrored large-scale at-sea surveys in Washington. Despite this consistent and ominous decline in overall murrelet density, the density of juvenile murrelets and murrelet productivity ratio (juveniles:adults) did not decline over this time period. Thus, the declining density of murrelets in the San Juan Islands was due to declines in adult murrelets only, not juveniles. Annual estimates of overall murrelet density were positively correlated with winter El Niño Southern Oscillation (ENSO) indices. We estimated that, on average, 6,605 (± 2,531 SD) murrelets occurred during surveys annually, confirming that the San Juan Islands contain some of the most heavily used marine areas in the portion of the U.S. range in which murrelets are threatened. In ENSO years, numbers increased to >8,500 birds. Heavy use of the San Juan Islands in ENSO years suggests that this area may provide refugia marine habitat for murrelets when prey availability along the outer Pacific Coast is poorer than usual.