We analysed the distribution of living larval Chironomidae (Insecta: Diptera) along a depth transect (0–80 m water depth) at Kigoma Bay in Lake Tanganyika (East Africa) to explore the ecological indicator value of Lake Tanganyika's midge fauna and to delineate the habitat preferences of resident larvae. Additionally, by comparing the taxonomic resolution reached in live versus fossil chironomid studies in this lake, we appraised the general information content of African fossil chironomid assemblages and, therefore, the quality of African chironomid-based palaeoenvironmental reconstructions. We found 141 chironomid specimens, representing two Tanypodinae, one Orthocladinae and 13 Chironominae (seven Chironomini and six Tanytarsini) taxa. All of these are conspecific to larval types encountered in subfossil collections from Lake Tanganyika or smaller East African lakes, but their differential diagnoses are updated here to include exoskeletal elements that are generally better preserved on live specimens. The chironomid assemblage collected in the Kigoma Bay depth samples is dominated by a few species of chironomine detritus and algae feeders, concentrated in areas of high macrophyte density. Additionally, there is a small component of tanypodine predatory taxa, along with several relatively rare, possibly habitat-specialist, taxa of both subfamilies. Our results further indicate that littoral and sublittoral palaeoenvironments in Lake Tanganyika may generally be inferred from high fossil density and diversity. The fairly high correspondence between inferred habitat preference of fossil and live collections in Lake Tanganyika indicates that, in large African lakes, the near-to-offshore gradient in chironomid habitat is imprinted on fossil assemblages. Hence, death assemblages deposited recently at various locations and microhabitats within Lake Tanganyika can be used as modern calibration data for palaeodepth inference. Moreover, Tanganyikan fossil-based taxonomy fully matches the taxonomic resolution reached in this study, so ecological information retrieved from live specimens can immediately be used for palaeoenvironmental studies.