Tanganyika is a marvellous lake in which to go snorkelling, or even scuba diving, as the numerous fish are beautifully coloured and there is seldom any need to dive deeply. That said, you must be aware of the risks – from crocodiles and hippos to bilharzia. Both animals can be very localised and, if bilharzia exists here, then it will also be patchy in its distribution.
There is also an endemic fish-eating snake, the Tanganyika cobra, which usually avoids swimmers like terrestrial snakes avoid walkers... but watch out for them anyhow. The locals obviously know the area, so if you are considering taking a swim then ask their advice about the precise place that you have in mind. They may not be infallible, but will give you a good idea of where is likely to be safe, and where is not.