Explanation:

- The river Yamuna: This phrase correctly introduces the subject of the sentence, the river Yamuna, without any grammatical flaws.

- has many non-native species: This part correctly states that there are several species not originally from the river, grammatically correct.

- that is affecting: This is where the grammatical error lies. "That" refers to "species," which is plural; therefore, it should be "that are affecting."

- its eco-system: This phrase is grammatically correct. It indicates the system's possession accurately.

Option 1 is correct because it contains the grammatical error.

.