the rocky basin
The sentence reads, "The lake’s rocky basin consists of three depressions, which hold a total volume..." The word "which" refers to the immediately preceding noun phrase, "the rocky basin.
it is near the sea
The passage states that researchers speculate the seals' ancestors migrated when the lake was connected to the sea. This implies it is no longer connected to the sea. The other options are true: it does have a great variety of fish (including the omu), it holds 20% of the world's freshwater (a very large amount), and it is estimated to be about 25 million years old
its ecosystem is special
The passage explicitly states, "To scientists, Lake Baikal is of particular interest because of its unique and isolated ecosystem." While it is isolated, the reason for scientific interest is the unique ecosystem.
an animal unique to the lake
The passage says, "Another creature that is unique to this Siberian Lake is the omu, a fish..."
transparent
The passage says, "For centuries, the water in Lake Baikal was so clear that it was possible to see down to depths of 40 to 60 feet." "Transparent" is a synonym for "clear" in this context.
dirty
The passage explains that certain organisms consumed material "that would otherwise cloud the water." "Cloud" in this context means to make the water less clear, or dirty. "Muddy" is a close synonym, but "dirty" encompasses a broader range of impurities that could cloud water, including bacteria and organic matter mentioned in the passage. Therefore, "dirty" is a slightly better fit.