Marine protected areas (MPAs) have been established to decrease the negative impacts of human activities on important marine habitats. Several sea turtle species reside within MPAs; however, analyses of habitat suitability for sea turtles within many MPAs is typically lacking. Habitat modeling and species mapping have become essential tools in determining areas suitable for species inhabitance. MaxEnt is a popular machine-learning program that uses presence-only occurrence data and is considered the best modeling method in discriminating between suitable and unsuitable habitats. Using MaxEnt, we created species distribution models (SDMs) from presence-only occurrence points for juvenile hawksbills and three environmental variables: boat traffic intensities, prey item distributions, and benthic characterizations, within the Sandy Bay West End Marine Reserve (SBWEMR) in Roatán, Honduras. Area under the receiving operator curve (AUC) values were greater than 0.75, indicating high model accuracy. Jackknife evaluations indicated algal prey item Dictyota spp., boat traffic intensity, and Geodia neptuni sponge abundance had the greatest influence on species distribution. Areas of suitability shifted based on time of day and ranged from a low probability of hawksbill presence (0.0) to a high probability of hawksbill presence (0.8). Regardless of time of day, the SBWEMR is classified as at least moderately suitable (>0.2–0.4), with least suitable habitat (0–0.2) prevalent in the most northeastern region of the reserve. The greatest suitability (>0.6–1) was evident within the mid-region and southern most regions of the reserve. Probability of hawksbill presence increased in accordance with increasing boat traffic, although there was no clear causative relationship between the two. Although the reserve overall is mostly moderately suitable, the SBWEMR remains an important local recruitment and foraging ground for juvenile hawksbills. Hawksbills have been considered resilient, continually functioning beneath their operational limits. However, with continued global depletion of essential habitats over time and lack of effective MPA management, areas of habitat suitable for hawksbill inhabitance may decrease below levels sufficient for hawksbill presence in protected areas of the Western Caribbean.