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New approaches to abundance surveying utilizing unoccupied aerial vehicles (UAVs) are proving to be effective tools in marine and terrestrial environments. We explored UAV efficacy for surveys in the Galapagos Marine Reserve (GMR), where relative abundance patterns of juvenile sharks and subsequent classifications of putative nursery areas based on environmental drivers are lacking. The UAV method allowed greater temporal and spatial coverage. We expanded classification of shark nursery habitat through monthly drone surveys and environmental data collection at 14 sites around San Cristobal Island (GMR) from November 2018 to July 2019. In the period of surveying, 56 flights identified 453 juvenile Carcharhinus limbatus (blacktip shark). Classification of nurseries followed three criteria, necessitating higher density, short‐term residency, and annual site fidelity in target locations. We developed preliminary generalized linear models to elucidate potential environmental parameters influencing the perceived abundance and habitat preference of juveniles. Four sites were identified as either potential nurseries or nursery areas for the target species based on previous excursions. An averaged model was subsequently created from the models found to best explain deviance patterns (R2 = 0.10–0.44) in perceived shark abundance and habitat preference. Relative variable importance (RVI) values further clarified the parameters most associated with higher juvenile presence. This approach provides a systematic method of abundance surveying while simultaneously beginning the process of defining when and where we expect to find higher abundance through environmental modelling of most influential parameters to perceived abundance in this environment. [ABSTRACT FROM AUTHOR]