Large East African Rift lakes have been changing rapidly during the last decades. They typically have a relatively high productivity compared to large temperate lakes and sustain active fisheries providing local populations with a relatively cheap source of proteins. However, human-induced changes, including climate change, can have significant negative effects on primary production of these lakes, as shown for Lake Tanganyika. It is likely that these decreases in primary production have affected secondary producers and fisheries, but, before being able to predict the extent of the primary productivity changes and how they affect whole ecosystem production, an improved understanding of ecosystem function and food web processes is required.