The distributions of shortfinned eels (Anguilla australis) and longfinned eels (A. dieffenbachii) of all sizes in three New Zealand coastal streams were investigated during summer by sampling stratified, randomly chosen pool, run, and riffle sites from tidal to upper reaches. In all streams, both species were widespread, although a greater proportion of the total population of shortfinned eels was present in the lower reaches and small eels (<300 mm total length (TL)) had advanced further up stream than longfins in two of the streams. The biomass (g m‐2) of longfinned eels <300 mm TL was greatest in riffles, whereas that of comparable‐sized shortfinned eels was evenly distributed across habitat types in all streams; in contrast, eels ≥300 mm TL of both species showed no consistent pattern of habitat use between streams. Multiple regression analysis of species biomass (g m‐2) for four size groups (<100; 100–199; 200–299; ≥300 mm TL) against 16 habitat variables, indicated that the distribution of shortfinned eels <300 mm TL was most closely associated with distance from the ocean, whereas that of longfinned eels of the same size group was most closely associated with water velocity and substrate. Medium‐large eels (≥300 mm TL) of both species were strongly associated with cover, with longfinned eels using a greater variety (macrophytes, banks, in‐stream debris, shade) than shortfinned eels (primarily riparian cover). Overall, our findings suggest that the longfinned eel is a more generalist species, living in a broad range of habitats, whereas the shortfinned eel is more specialised, as is reflected in differences in their distributions and habitat associations.