Bilharzia does exist in the lake. Best bet is to swim away from the populated areas (semi-hard to do in that area of the lake - but any trip out snorkling will be away from the shore, so more than likely you would be fine), and to avoid the grassy reeds where the snails like to live. There's also easy access to a pill here (Praziquantel) that you can take 6 weeks later which would kill any bug that you may (however unlikely) have contracted.

Hippos are in very isolated areas of the lake, have never been a huge concern. There's a small pod that stick around a marshy area 10km or so away from the Cape Maclear area - haven't heard of them getting near people around the beach / snorkling areas. Crocs again are in very isolated areas of the lake. Usually they are around the mouths of the rivers/streams after rainy season.

In sum - All of those things are there, and can be of a concern, but are easily avoidable. They are quite low risk, but of course there is still a risk, so comes down to ones personal tolerance. Cape Mac is a great little spot on the lake, and I try and make it down there a couple times a year (I'm based in Lilongwe, so we often go to areas around Senga Bay as it's a bit closer for weekend trips). Fine for water activities (hey, you're on the lake!) and the views are stunning - especially when you get just offshore (Thumbi Island / Mumbo / Domwe / etc). If you are still super concerned about crocs or hippos, you can ask when / where the last sighting was - but just know that they are not a common occurrence around that area.


Now if you were thinking of swimming in the Shire River, that's a different story.