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• We introduce an innovative habitat selection framework for marine tracking data. • Coastal fringing vegetation drives space use in a juvenile elasmobranch. • Juvenile sharks avoid once-pristine areas, now human coastal development sites. • Establish shark behaviour as indicator of habitat quality and area for protection. • Findings have regional and global implications for the management of coastlines for sharks. Nearshore environments represent important habitat for many marine vertebrates during their early-life stages. Globally, these coastal sites are impacted by human activities that have the potential to negatively impact biodiversity in ways we do not yet fully appreciate. To improve our understanding of the relevance of mangrove removal in tropical elasmobranch nursery grounds, we studied the globally Vulnerable lemon shark ( Negaprion brevirostris ) in a mangrove-fringed lagoon in Bimini, The Bahamas, following a decade of coastal development and habitat disruption. We used two years of acoustic telemetry detections and generalised linear mixed models (GLMMs) to evaluate the link between juvenile shark spatial behaviour and six features of their physical environment. AIC-adjusted model-averaged predictions of habitat selection demonstrated that distance from the central mangrove forest was the most important feature for sharks. After updating model averaging to account for overall preference for proximity to the central forest, we found that medium density seagrass was secondarily preferred over all other habitat types (bare sand, sargassum, urban and rocky outcrops, and deep water) within the core use area (probability of use ≥ 50 %). Locally, our results support including this core area in future marine protected area considerations. More broadly, in the face of rapid global population declines of many elasmobranchs and wide-spread habitat fragmentation in coastal marine nurseries, we identified widely applicable habitat features underpinning an area of high ecological significance for a threatened shark during a vulnerable life stage and outlined a habitat selection framework suitable for using marine vertebrate movement data as ecological indicators for future applied conservation.