In freshwater lakes, water level variability is a key driver of functional connectivity through its influence on the distribution, complexity and connectedness of physical habitat patches, and animal behaviour. The concept of ‘functional connectivity’, integrates both physical connectivity among habitat patches and species-specific traits (e.g. dispersal ability), providing a holistic view of how animals interact with their environment. We investigated the influence of lake level variability on functional connectivity among four lakeshore habitat types (emergent vegetation, submerged-emergent vegetation complex, bare sediment and pier habitat types), at inter- and intra-lake scales, in Lakes Albert and Alexandrina at the terminus of the River Murray, South Australia, using small-bodied fish assemblages as a biotic model. Small-bodied fishes were sampled, using a suite of fyke nets and box traps on four occasions, during high, medium and low water levels. A total of 13,280 fish were sampled from 19 species, of which five dominated numerically (84 % of the assemblage). These species can be considered ecological generalists, and generally, utilised all habitats equally. Conversely, the rarer species are considered to exhibit more specialist habitat requirements and life history traits, and were more common in the emergent-submerged vegetation complex habitat, with greater connectivity to other habitat patches. Patterns associated with water level were complex and difficult to disentangle from other factors (e.g. habitat type) and our lowest sampled water level did not disconnect habitats as predicted. Notwithstanding, we suggest that submerged macrophytes are a vital habitat component for small-bodied fish in freshwater lakes and that the loss of this habitat component would have significant negative consequences for biodiversity. The management of freshwater lakes, particularly water levels, should look to promote submerged-emergent macrophytes habitat complexes and connections among such habitat, and in association, diverse small-bodied fish assemblages.