A GIS model of the littoral bathymetry and substrate composition of Lake Taupo was created using ArcInfo. Littoral substrates were mapped by aerial photography and confirmed by ground‐truthing. Water depths were determined by echosounding linked to a differential GPS. These data were imported into ArcInfo where a 3D GIS model was used to calculate the total area of smelt, Retropinna retropinna Richardson, spawning habitat (i.e. clean sand between depths of 0.5–2.5 m) at each of five lake levels. There was little change in area over the first 50 cm below the natural maximum lake level, but spawning habitat decreased rapidly over the next 1.4 m such that a 30% reduction occurred at the natural minimum level. Anecdotal information on inter‐annual variations in lake level and smelt abundance supported the notion that high lake levels in spring result in high recruitment of smelt. The GIS model also predicted effects of lake level change on areas of macrophyte cover and on other littoral substrates, and could be used to assess effects of lake level changes on the habitats of other biota.