Native speakers also find that sentence clumsy, confusing, or even ungrammatical. Perhaps the author made it that way deliberately, for artistic reasons, or perhaps it was just some sloppy writing that the copyeditor didn't fix.
Here's my attempt to rewrite it to make it clearer:
There were deep creases in the river's surface where it went round rocks, and there was a hollow, clunking noise.
Yes, the original sentence means that the river flowed around a patch of rocks.
The author wrote when to introduce the place where the deep creases were. Normally we would say where. It's not unusual in English to swap words for time with words for space, but in this sentence it's jarring.
When I first read the sentence, I thought it was ungrammatical because I couldn't find a verb that said anything about a hollow, clunking noise. At first, "a hollow, clunking noise" appears to be a second object of "went round", but that doesn't make sense: a river can't "go round" a noise.* Later, I noticed that the sentence as a whole is structured like this one:
There were three Queens and a Jack.
"Three Queens" corresponds to "deep creases when it went round rocks." "A Jack" corresponds to "a hollow, clunking noise". When the sentence is this short, it's easy to see that "three Queens" and "a Jack" are both subjects of the verb "were". In the original sentence, a reader tends to see "deep creases" as the whole subject of "were": "deep creases" has sort of "used up" the verb "were" in the reader's mind. People don't think about this consciously when reading, of course, but the result is that the reader is likely to feel lost upon reaching "hollow, clunking noise". The feeling of disorientation happens because that phrase doesn't seem connected to a verb.
That isn't wrong, it's just unnecessarily confusing. In my rewrite, I added there was to make the sentence easier to follow. In the original, the plural "were" led the reader not to connect it with "a hollow, clunking noise" so many words later, after a plural subject ("creases"). The singular "was" agrees with the singular "hollow, clunking noise", so the reader never gets lost. (This shows how there is more to English grammar than precise rules, and there are no exact boundaries between grammar, style, and clarity.)
*By the way, people seldom use "round" as a preposition in the United States, so Americans might be more likely to judge the sentence ungrammatical. I just figure that the author is likely to be British.