Vertical profiles of temperature, dissolved oxygen (DO), conductivity and pH in the water column of Lake Chala, a small (4.2 km2), deep (~90 m), and permanently stratified tropical crater lake at ~880 m above sea level in East Africa (3°19'S, 37°42'E), were measured at 2 m intervals through the upper 50 m of the water column at monthly intervals between September 2013 and January 2015. In the same time interval, suspended particulate matter (SPM) was collected monthly at 13 discrete depths by filtering 5-10L of water over pre-combusted glass fibre filters. The concentration and fractional abundance of branched glycerol dialkyl glycerol tetraethers (brGDGTs) in SPM was analysed for all depths for the months November 2013 and August 2014, and at 0, 10, 25, 35, 50, 60, 70, and 80 m depth for all other months (total n= 146). The brGDGTs were analyzed using ultra high performance liquid chromatography-mass spectrometry, separating 5-methyl and 6-methyl brGDGT isomers.