Controlling pathogens within the aquaculture systems is important to prevent their impact on both human health and wild native populations. It is not uncommon for aquaculture ponds to contain undesirable species of fish which can compete for food or space with the farmed fish or play a role as a reservoir of diseases. The aims of this study were to determine the occurrence of parasites in undesirable species of fish commonly found in Australian Murray cod farms in New South Wales to determine if they can act as a reservoir for important parasites. In the present study, a total of 106 Australian smelt (Retropinna semoni), and 144 gudgeons (Hypseleotris spp.) were sampled from Murray cod ponds for parasitic infections. These fish are among the most common undesirable fish found on Murray cod farms in the region. No metazoan parasites were found in Australian smelt. One hundred and nine gudgeons were used for parasitology and 35 for histology. Parasites were examined morphologically followed by analyses of their DNA sequence data. Seven percent of infected gudgeons (out of total 109 examined) had externally visible signs of parasitic infection. The gudgeons had high parasitic burdens with 89.9% containing encysted metacercaria, identified as Apatemon hypseleotris, belonging to the family Strigeidae, 41.3% non-encysted metacercaria identified as Clinostomum sp., belonging to the family Clinostomidae, 6.4% (larval) cestodes identified as the metacestode of the genus Parvitaenia, belonging to the family Gryporhynchidae and a single Camallanus larval nematode (0.9%), all known to be of low host specificity and potentially transmissible to Murray cod. Histopathology results showed the presence of an additional parasite, a monogenean parasite in the gill. Some of the parasites found in the present study can be pathogenic for infected fish. This study provides critical baseline information on the occurrence of parasites in wild reservoir fish on Murray cod farms. Further research is needed to understand the potential risks to Murray cod populations in farm systems as well as to other fish in natural water resources where Murray cod are released.