A person trying to parse this sentence as a non-native English speaker (and possibly not from a Christian cultural/religious background) might encounter two things. Here's what I infer from it:
> > … As much mud in the streets as if the waters had but newly retired from the face of the earth, would not be wonderful to meet a Megalosaurus, forty feet long or so, waddling like an elephantine lizard up Holborn Hill.
1. 'as if the waters had but newly retired' - this is clearly an allusion to the Christian biblical story of the Flood, Noah's ark, etc. The book was written in an era and for a target audience where the educated readers were almost all certainly regular dedicated Sunday church-goers.
2. It helps to understand the relatively recent 'discovery' of dinosaur fossils at the time the book was written, the beginnings of scientific understanding of them, and the history of Paleontology from approx. 1800 to 1900 to understand the reference to the Megalosaurus. It's my understanding that the book was written at a specific moment in history when the discovery of dinosaur fossils was a hot new scientific fad and would be reported on in the popular press.
Now if you're a person who is highly literate in English but you haven't specifically studied the history of how weird English people started going off to the far corners of the earth and digging up dinosaur bones and scientifically categorizing them (see section for 19th century here: https://en.wikipedia.org/wiki/History_of_paleontology ), and you don't get the part about 'the waters' meaning a reference to an entire planet wide flood in a religious myth, the whole sentence is not going to mean the same thing.
It's not that a highly literate English reader from, let's say, Bangladesh won't understand the words in the sentence, but a great deal of the underlying meaning will be lost. Much as you or I might not understand the metaphors, allusions and allegories in poetry or literature written 150 years ago in a foreign language.