Advances in food web modelling are revealing the characteristics of ecological communities that are related to stability and underpin their biodiversity. A key future research topic is the incorporation of intraspecific trait variability into our understanding of food webs. We explore the conceptual linkages between food web modelling and intraspecific differences in behavioural traits (e.g. animal personality). Specifically we describe the potential for intraspecific behavioural variation to be a stabilizing force in food webs, both as a source of within-species variability in food web interactions and by facilitating adaptive responses to changes in the trophic environment. We empirically investigated these conceptual links between food webs and behavioural traits, by studying the aquatic communities in Australia’s arid-zone and populations of Australian desert gobies (Chlamydogobius eremius). This included community-level food web analysis conducted alongside individual-level analysis of goby’s trophic position and behavioural traits. Our food web analysis revealed the importance of resource segregation and between-individual differences in trophic position to the stability of desert goby populations. Furthermore, behavioural traits (e.g. boldness, activity and exploration) varied within and between goby populations. Variance in these behavioural traits was closely linked the local trophic environment of goby populations. These results show that incorporating individual-level behavioural traits represents a promising area for food web research, and further highlights the importance of aquatic food web studies to the development of community ecology.