Understanding how endangered marine species rely on coastal habitats is vital for population recovery planning. The smalltooth sawfish (Pristis pectinata) is one of several critically endangered sawfishes worldwide known to use estuaries and rivers during their early life history. In a Florida estuary designated as critical habitat by the USA government, juveniles were monitored to characterise seasonality, recruitment, and habitat use. Stretched total length ranged from 671 to 2172 mm (n = 137, mean = 1248 mm). Sawfish were captured year round. Captures of neonates with embryonic rostral sheaths allowed refinement of the size at birth (671–812 mm) and confirmed a protracted timing of parturition (November–July), which peaked between April and May. Although sampling occurred throughout the estuary, five locations had the greatest catch rates. Most juvenile sawfish had an affinity for water 30°C, dissolved oxygen >6 mg L–1, and salinity between 18 and 30. Greater catch rates for sawfish >1 year old were associated with shoreline habitats with overhanging vegetation such as mangroves. These results detail habitat use within a recognised nursery that can be used for conservation of the first endangered marine fish species in the USA.