This study aimed to investigate the links between parasites and behavioural traits of juvenile Murray cod (Maccullochella peelii). The Murray cod is an endangered Australian freshwater fish for which restocking programs are in place and there is a growing human consumption market. However, little is known about the parasites of these fish and how these parasites influence their behaviour and survival. Fingerlings and yearling fish were sourced from a hatchery and the wild, and after acclimatisation in the laboratory, variation in behavioural traits was examined using emergence, exploration and predator inspection tests. The fish were then euthanised to determine their age and examined for infection with parasites. Wild fish had more camallanid nematodes and lernaeid copepods than hatchery fish. An information theoretic approach using Akaike’s Information Criterion (AIC) indicated that infection with protozoan cysts was an important factor for predicting the latency to emerge and explore a new environment, which was interpreted as reduced “boldness”. In contrast, the presence of lernaeid copepods was included in two of the four best models predicting predator inspection, indicating that infected fish were less likely to inspect a predator. Source of fish (wild or hatchery) was found to be a strong influence on behavioural responses in all our tests. All parasites found in the present study are known to result in clinical signs of diseases in their fish hosts, raising the possibility that responses in tests of behavioural traits reflect side effects of infection. Additionally, the effect of host adaptation to not show signs of parasite infection, or more simply that the effects on behaviour are subtle and difficult to reveal with small sample sizes, is discussed. Nonetheless, we propose that it is important that infection with parasites is considered in fish behavioural studies both to assess survival behaviour and to avoid misinterpretation of behavioural tests of animal personality.