Branched glycerol monoalkyl glycerol tetraethers (brGMGTs) are membrane-spanning lipids which were initially identified in marine settings and have more recently been found in peats and lake sediments . In the latter settings, their abundance relative to that of the branched glycerol dialkyl glycerol tetraethers (brGDGTs) appears to increase under warmer climate conditions. Furthermore, their relative distribution in bottom sediments from an altitudinal transect of East African lakes has been linked to local mean annual air temperature (MAAT). To shed light on their sources and identify potential environmental factors driving their production in lakes, we investigated their occurrence and distribution in the water column, surficial lake-bottom sediments, and catchment soils of Lake Chala, a permanently stratified (meromictic) tropical crater lake in East Africa. Data from the water column comprise both suspended particulate matter (SPM) collected monthly at eight depth intervals between 0 and 80 m for 17 consecutive months, and settling particles collected monthly at a depth of 35 m over a period of 53 months. In catchment soils, brGMGTs are either relatively scarce or absent. In the water column, their occurrence is dominated by four of the seven known brGMGTs and mostly limited to the anoxic zone. Whereas the spatial distribution and concentration of brGMGTs in SPM were strongly influenced by the seasonal cycle of strong water-column stratification alternating with deep mixing, this trend is not consistent on the multi-year timescale of the settling-particles record. Moreover, their relative distribution in both SPM and settling particles did not respond to temperature variation during the studied interval. In contrast to the water column, surficial lake-bottom sediments contain the full suite of known brGMGTs in a distinct and spatially uniform fractional abundance, strongly suggesting that the majority of brGMGT production takes place there. BrGMGT-inferred MAAT for the Chala area reasonably estimates measured MAAT and conforms to the East African lake brGMGT calibration. Our results have important implications for the use of brGMGTs as proxy for MAAT, in that outside of the equatorial zone the presumably greater offset between bottom-water temperature and MAAT may create a bias towards cold-season air temperature. Regardless, the more singular source of brGMGTs in lake sediments is an advantage for paleotemperature reconstruction compared to brGDGTs, which several studies now indicate to have a mixed aquatic and terrestrial source of which the relative contribution cannot easily be disentangled or assumed to have been constant through time.