The day‐time cover preferences of three size groups (small = <100; medium = 100–199; large = 200–299 mm total length (TL)) of juvenile shortfinned eels(Anguilla australis)and longfinned eels(A. dieffenbachii)were tested during summer in replicate channels provided with natural (macro‐phytes, woody debris, cobbles) and artificial (shade, plastic pipes) cover types. Tests on the longitudinal distribution of all three size groups of shortfinned eel (with no cover in the channels) revealed no significant bias in the distribution of small and medium eels, but did so for large eels which favoured the ends of the channels. Similar bias occurred in the actual cover preference tests, which was adjusted for by the Poisson log‐linear model used in analysing the data. When the species were tested separately, small and medium eels of both species preferred cobbles and macrophytes more or less equally, whereas large eels showed a clear preference for macrophytes and a minor attraction for cobbles. When tested together, species cover preferences differed significantly, with a greater proportion of all sizes of longfins in the cobbles and shortfins in the macrophytes and woody debris. Artificial cover was an unattractive alternative to natural cover for all sizes of both species of eel. The results of these experiments suggest that both size and species interactions influence the distribution of juveniles of both species in the wild.