The habitats used by shortfinned eels(Anguilla australis(Richardson)) in Lakes Ellesmere (Canterbury) and Waahi (Waikato), New Zealand, were determined using a variety of capture techniques during the summers of 1994/95–1997/98. The most successful technique used to catch juvenile eels (<300 mm total length (TL)) in Lake Ellesmere was a 2‐m wide beam trawl; larger eels were captured mainly by fine‐meshed fyke nets. Trawl catches during the night exceeded catches during the day by a factor of 2.4. In Lake Ellesmere, juvenile eels were mainly caught in the depth range 0.6–1.2 m, on a gravel and/or mud substrate, and within 1 km of the shore. In contrast, larger eels (>300 mm) preferred sandy substrates, but showed no marked preference for particular depths or distances offshore. The spatial distribution of both size groups was non‐random. Although water temperature did not influence catch rates (CPUE, catch‐per‐unit‐effort) of either size group, catches of the smaller eels were greater during the new moon phase than during the other phases—catches of larger eels were unaffected by lunar phase. Length‐frequency distributions of eels from Lake Ellesmere were strongly bimodal, with eels 200–300 mm poorly represented—this probably reflects poor recruitment for several years, either because lake opening times did not coincide with the availability of glass eels, or because overall numbers of glass eels were low. Juvenile eels in Lake Waahi, caught in fine‐meshed fyke nets and in special brush collectors, were also inshore residents; unlike Lake Ellesmere, juvenile eels could be caught at the lake margins, probably because Lake Waahi is not subject to the same wind‐induced water level fluctuations as Lake Ellesmere. Recruitment into Lake Waahi commenced in mid December, but there was evidence of low recruitment in past years for this lake also. An important outcome of this research is that estimates of the number of juvenile eels to be transplanted during stocking programmes should be made using the area of the shallow littoral rather than the area of the whole lake.