Bluefin Tuna Thunnus thynnus are highly sought after in commercial and recreational fisheries along the East Coast of North America. To appropriately assess and manage Atlantic Bluefin Tuna (ABT), it is necessary to understand their habitat use during multiple ontogenetic stages. We tagged 17 juvenile ABT in the northwest Atlantic Ocean with pop-up satellite archival tags (PSATs) to determine environmental factors that may affect habitat use. The PSATs were deployed off the coast of Massachusetts in August and September 2012. A generalized linear mixed model was applied to determine factors affecting the mean depth occupied by fish, and beta regression was used to understand factors affecting the proportion of time spent below the thermocline. Thermocline depth significantly affected the mean depth occupied by juvenile ABT and the proportion of time they spent below the thermocline. Time period (dawn, day, dusk, and night) also significantly affected the mean depth occupied by juvenile ABT. Additionally, the time period × lunar illumination interaction had a significant effect on the proportion of time spent below the thermocline. This study is the first to demonstrate that environmental factors such as thermocline depth, time period, and lunar illumination can significantly impact vertical habitat use by juvenile ABT and demonstrates the utility of generalized linear mixed models for investigating fish habitat use.