Objective The aim of this study was to determine baseline reference data for morphometric measurements and haematological and plasma biochemical parameters in clinically healthy eastern water dragons (Intellagama lesueurii lesueurii), accounting for the variables of season and sex. The clinical objective was to provide clinicians and researchers with baseline reference intervals (RIs) in order to assess accurately the health of a population or individual animals. Methods The study group comprised 39 free‐ranging eastern water dragons. To monitor seasonal changes in data two study periods were assigned: September–October 2009 (spring) and January–March 2010 (summer). The 18 males and 21 females were captured in the grounds of Taronga Zoo, Mosman (33°50′45′′ S, 151°15′20′′ E) in Sydney, New South Wales, Australia. Basic morphometric, haematological and plasma biochemical parameters were measured. RIs were generated in accordance with the American Society of Veterinary Clinical Pathology guidelines. Data were analysed for the effects of sex, season and sex–season interactions using restricted maximal likelihood modelling. Results Reference values were established in eastern water dragons for morphometric data and RIs were generated for haematological and plasma biochemical levels. The study showed seasonal variation in uric acid. Weight, total length, snout–vent length and basophil % showed significant differences according to sex. Sex–season interactions were detected for calcium, monocyte % and total protein (refractometry). Conclusion Multiple parameters exhibited normal physiological variation between season and sex and an interaction between the two factors. These variables need to be considered in the clinical context when interpreting results of haematological and biochemical analyses in eastern water dragons. The RIs established from this population will provide a basis for further studies in both free‐living and captive eastern water dragons, and for comparison in clinical cases.