Habitat Conservation Plans (HCPs) commonly facilitate habitat conservation on private land in the United States, yet the effectiveness of individual HCPs is rarely evaluated. Here, we assess the effectiveness of a high-profile HCP created by a lumber company to protect old-growth forests used for breeding by Marbled Murrelets (Brachyramphus marmoratus) on private land. We used 17 years of HCP-monitoring data to compare trends in murrelet occupancy and inland counts between private HCP areas and public reference areas over time. Based on occupancy models applied to audio-visual survey data, average occupancy was higher in public reference areas (0.85; 85% confidence intervals [CI]: 0.79–0.90) than in private HCP areas (0.46; 85% CI: 0.38–0.54). Numerically, trends in occupancy were slightly positive in public areas (= 1.01; 85% CI: 0.94–1.08) and slightly negative in private areas (= 0.97; 85% CI: 0.87–1.06), but CI did not preclude stable occupancy on both ownerships. Based on generalized linear mixed models applied to inland radar survey data, murrelet counts in private HCP areas (least-squares [LS] mean = 8.7; 85% CI: 6.2–12.2) were lower than those in public reference areas (LS mean = 14.8; 85% CI: 10.1–21.7), but CI overlapped. Murrelet counts declined by 12–17% annually on both ownerships over the study period based on the top model, but a closely competing interactive model suggested more rapid declines in public reference (14–20%) than in private HCP (10–15%) areas. Both models indicated that murrelet counts were negatively related to sea surface temperature, suggesting that warm ocean conditions negatively affect murrelet breeding effort. Collectively, these results suggest that while HCP habitat may be lower quality than public reference areas, the HCP has likely not exacerbated ongoing declines of murrelets in the region. This work highlights the importance of including reference areas when evaluating conservation policies.