Sediments from Lake Te Anau comprise predominantly mineral components derived from the breakdown and weathering of the surrounding metamorphic country rocks, and a smaller biogenic silica component (mainly diatoms). Sedimentological and micropalaeontological analyses permit the differentiation of the samples into two types. First, sediments from river deltas and headwaters are characterised by high inputs of organic matter (up to 9%) and sandy to gravelly material. The amount of diatoms in these sediments (0.5–1% by volume) is by far outweighed by clastic components. Second, sediments from deep basins are more fine‐grained and fairly uniform in mineral and grain size composition with a relatively high organic carbon content (1–2%) in the clay fraction. The diatom content in the deep basin sediments is on average higher (5–10% by volume) than in the headwater samples owing to less dilution by clastic components. Nonetheless, the sediments in most of the lake basins appear to be predominantly allogenic. Endmember analysis of the compositional data groups the clastic sediments into five types depending on the surrounding source rocks for these sediments. The remoteness of the lake, the composition of its sediments, and their predominantly allogenic nature suggest that the lake could serve as a baseline for future global pollution studies.