I am confused with the following sentence. would anyone explain its structure, please?
There is more than 50 times as much freshwater stored underground than in all the freshwater rivers and lakes at the surface.
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The cited text is actually syntactically invalid. It's a little tricky to explain exactly why, but I'll try to do it using some examples of similar constructions...
1: There is more than a litre of water in this jug
(The amount of water in this jug exceeds one litre)
2: There is more sea water than [there is] fresh water
(The amount of sea water exceeds the amount of fresh water)
3: There is as much as I need
(The actual amount is enough - it's equal to the amount that I need)
4: There is more than I need
(The actual amount exceeds the amount that I need by some unspecified factor)
5: There is twice / three times as much as I need
(The actual amount is double / three times the amount that I need)
6: There is more than twice as much as I need
(The actual amount exceeds double the amount that I need)
...where the second occurrence of there is in #2 would often be "deleted" (not explicitly stated, because it's a predictable element within a "parallel" construction).
If we break down the constituent parts in OP's example, the information we're being given pragmatically implies the following "background facts"...
a: "underground" fresh water exists
b: "surface" fresh water [also] exists, in rivers and lakes
...where the relative amounts of (a) and (b) are being compared. Hopefully, if you consider the highlighted elements in my examples, you'll be able to see why OP's example should be corrected to...
There is more than 50 times as much freshwater stored underground
thanas [there is [stored]] in all the freshwater rivers and lakes at the surface.
(Either or both [there is] and [stored] are "predictable" repeats, that may be optionally "deleted".)
The substantive assertion (the reason someone wrote OP's example in the first place) states that the amount of fresh water stored underground greatly exceeds the amount on the surface (it's over 50 times greater).