If there isn't sewage or livestock runoff entering the lake, the problem is caused by wildlife. Almost all animals carry e. coli and other bacterial or protozoan infections. Deer, beavers, rodents, all of them. Cattle have a large concentration, so if livestock runoff is entering the lake, that's likely it. Unless large amounts of livestock or inadequately treated wastewater are entering a lake, virtually all contaminants are naturally occuring in either the soil or ambient wildlife.
Tyler