The benefits of marine protected areas are difficult to estimate for mobile species, but their effectiveness can be increased if essential habitats, such as nursery areas, are protected. In the present study we examined movements of juvenile blacktip reef (Carcharhinus melanopterus) and sicklefin lemon (Negaprion acutidens) sharks in a coastal nursery in northern Australia. Telemetry-derived data were modelled using Brownian bridges and overlaid with maps of habitats and no-take zones. Juvenile N. acutidens were typically residents (≥30 days) of the nursery with small areas of core space use (<1.9 km2), whereas juvenile C. melanopterus were non-residents (<30 days) and used larger areas (<5.6 km2). Both species exhibited positive selection for sandflats and mangroves, and avoidance of deeper lagoonal and slope habitats. Monthly patterns were examined only for resident N. acutidens, and residency decreased with increasing shark length and varied seasonally for males but not females. Space use showed weak declines with increasing tidal range, and slight increases with mean air pressure, rainfall and shark length. Protecting sandflat and vegetated habitats may increase the efficacy of no-take zones for juvenile N. acutidens, because they exhibit residency and affinity to these features. Conversely, such protection will be of limited benefit for juvenile C. melanopterus, because they exhibit low residency and broader movements.