The distribution of isoprenoid and branched glycerol dialkyl glycerol tetraether (GDGT) lipids was studied in material from various sources in and around Lake Challa, a crater lake on the southeastern slope of Mt. Kilimanjaro (Tanzania), to examine the provenance of GDGTs in lake sediments and their potential application as palaeoenvironmental and palaeoclimatic proxies. The study material included samples collected at monthly intervals in a sediment trap over one complete annual cycle, particles suspended in the stratified water column, profundal surface sediments, and soils surrounding the lake. The sediment trap time series revealed that crenarchaeol and related isoprenoid GDGTs were predominantly produced in January and February, following the locally prominent short rain season (November-December). The TEX86-inferred temperature derived from sedimenting particles corresponded well with lake surface-water temperature at this time of largest crenarchaeol flux. Molecular ecological analysis showed that Group 1.1a and 1.1b crenarchaeota are the most likely source organisms of these GDGTs. GDGT-0 in the lake sediments does not only originate from lake surface-dwelling crenarchaeota but seems predominantly derived from archaea residing in the deeper, anoxic part of the water column. The main flux of branched GDGTs to the sediment was during the short rain season and is most probably derived from eroded catchment soils in surface run-off. However, a contribution from in-situ production of branched GDGTs in the lake sediment or water, or in groundwater cannot be fully excluded. We conclude that palaeoclimatic reconstruction based on branched GDGT distributions in lake sediments should only be performed when the origin of those branched GDGTs is well constrained. (c) 2009 Elsevier Ltd. All rights reserved.