A lotic ecoregion classification for New Zealand was developed based on six macro-environmental variables; vegetative cover, bedrock geology, soils, relief, rainfall normals, and Meteorological Service Climatic Regions. South Island maps of these variables were merged, and a new composite ecoregion map generated using a GIS. Twenty-five ecoregions are proposed, 13 in the North Island and 12 in the South Island. The water chemistry and benthic invertebrate assemblages of 100 small headwater streams within 10 of the South Island ecoregions were investigated to test the validity of my proposed ecoregions. Most ecoregions could be recognised by characteristic assemblages of invertebrates. The "pristine" forested ecoregions of Westland, North-west Nelson, North-east Nelson, and the South-east Forest had high taxonomic diversity, numerous endemic species, and faunas dominated by mayflies and stoneflies. In contrast, the anthropogenically modified pastoral ecoregions of the East Coast Plains, Central Otago, and the Southland Plains had streams with very similar invertebrate assemblages, low taxonomic diversities and a predominance of molluscs, oligochaetes and dipterans. Streams in these ecoregions could only be distinguished on the basis of differences in the abundances of several common taxa. Water chemistry distinguished between ecoregions less successfully, however, South-east Forest and North-east Nelson streams in particular, were distinctive. Differences in the geology of catchments, in particular the presence or absence of alluvia, mudstone, soft sedimentary rocks and volcanic rocks have important influences on the water chemistry of South Island streams. An investigation undertaken in one ecoregion indicated the need for an ecoregion classification to take account of variations in land use. Thus, both invertebrate assemblages and water chemistry differed in streams draining catchments with four kinds of land use. Native forested streams had the highest taxonomic richness and faunas dominated by mayflies and stoneflies. Streams in exotic forest and scrubland catchments had progressively fewer taxa, particularly mayflies and stoneflies; streams in pastoral land had even fewer taxa, mayflies and stoneflies were rare, and molluscs and oligochaetes predominated. In summary, my ecoregion and land use investigations indicate that three macro-environmental factors; biogeographical events, climatic conditions, and vegetative cover/land use, are of primary importance in determining invertebrate assemblage structure and regional differences in the biotas of small, South Island streams.