The concentration and fractional abundance of bacterial branched glycerol monoalkyl glycerol tetraethers (brGMGTs) were investigated in the suspended particulate matter (SPM), settling particles, soils and surficial lake-bottom sediments of Lake Chala, a meromictic crater lake with a maximum depth ~90m, on the border of Kenya and Tanzania. The proportion of the brGMGTs relative to the branched glycerol dialkyl glycerol tetraethers (brGDGTs) is also reported (%brGMGT). This research was carried out order to investigate the sources and drivers of brGMGT production in lakes. For the SPM, 5 to 10 L of water were collected at 13 depths throughout the water column on a monthly basis between September 2013 and January 2015. A UWITEC double-funneled sediment trap of 86 mm diameter was used to capture settling particles during the period September 2010 until January 2015. Soil samples used in this study were collected by Buckles et al. (2014) (https://doi.org/10.1016/j.gca.2014.04.042) from various locations within and around the crater catchment of Lake Chala. Surficial lake-bottom sediments were collected by Buckles et al. (2014) in January-February 2010, by gravity coring at three different water depths.