Understanding how personality differences in animals develop and the broader significance of personality within ecology is an exciting challenge for researchers. Our study explores the importance of personality in the novel aquatic ecosystems of the Lake Eyre region in arid Central Australia. This region’s complex system of groundwater springs and ephemeral rivers contains habitats that contrast markedly in their abiotic and biotic characteristics. Using the Australian desert goby (Chlamydogobius eremius), a fish species that occupies this diverse range of habitats, we investigated how individual personality traits vary among several populations. We found evidence of significant differences both within and between goby populations across various behavioural axes (i.e. boldness and exploratory traits), suggesting that these traits are both ecologically meaningful and subject to selective pressures for these goby populations. In addition, we harness our concurrent research on the food-web and community ecology of these ecosystems to demonstrate the potential importance of an animal’s trophic environment to its behavioural phenotype, particularly with regards to boldness.