Yes the use of 'it' in the first example is ok.
Both the sentences are a little ambiguous though, as the last poster pointed out.
More than 300 rivers drain into Siberia's Lake Baikal, which holds 20 percent of the world's fresh water, more than all the North American Great Lakes combined. - this sentence sounds as though this lake has more rivers draining into it than all the North American Great Lakes combined.
The way to phrase this sentence to give the meaning you require is:
With more than 300 rivers draining into it, Siberia's lake Baikal holds 20 percent of the world's fresh water, which is more than all the North American Great Lakes combined.