が after "freshwater" is used as a postpositional particle which is placed after a subject and が after "likes" is used as a conjunctive particle which means "but".

The word 好き in Japanese, which roughly translates as "like/be fond of" in English, does not function as a verb as it does in English, but rather an adjective. So the object that is being liked is indicated using が. This ”noun + が + adjective" construction is often used. For example: その建物が高いです。 That building is tall. リーさんが大人しいですね。 Mr. Lee is quiet isn't he. あの猫が可愛い。 That cat is cute. I hope this answers your question. Please let me know if there is anything more you do not understand.

金魚は　たん水が　好きですが、かい水が　あまり好きじゃないです が before たん水 and かい水 is an object marker whereas が after 好きです is a contradictory conjunction. (金魚 is a topic.) A goldfish likes freshwater, but doesn't like sea water. With some kind of adjectives, が leads an object. Those adjectives mostly describe emotions. わたしは　にほんごが　すきです。 私は日本語が好きです。 I like Japanese. わたしは　へびが　きらいです。 私は蛇が嫌いです。 I hate a snake. わたしは　ゆびわが　ほしいです。 私は指輪が欲しいです。 I want a ring. わたしは　ゆうれいが　こわいです。 私は幽霊が怖いです。 I'm afraid of a ghost. わたしの　ともだちは　うたが　じょうずです。 私の友達は歌が上手です。 My friend is good at singing. わたしは　えいごが　とくいです。 私は英語が得意です。 I'm good at English. I can finish answering your question here, but I'm going to add more. There is a typical sentence structure where は and が are used. X　は　Y　が Z。 This structure seems to be the same as your example sentence, but actually it's not. This が is a subject marker not an object marker. A topic is X, and Y is a part of X and "Yが Z" describes X's characteristic. ぞうは　はなが　ながいです。 象は鼻が長いです。 As for an elephant, its nose is long. かのじょは　かみが　くろいです。 彼女は髪が黒いです。 As for her, her hair is black. I hope this helps.

Hello. Let me try to explain this question for my study as well. a. 金魚は たん水"が"好きですが、かい水"が"あまり好きじゃないです。 First of all, it may confuse you more, but this is not natural expression. We use these 3 patterns [b] - [d] below instead of the above [a]. b. 金魚は たん水"が" 好きですが、かい水"は" あまり好きじゃないです。 c. 金魚は たん水"は" 好きですが、かい水"は" あまり好きじゃないです。 d. 金魚は たん水"は" 好きですが、かい水"が" あまり好きじゃないです。 You can see "が" isn't repeated in these 3 sentences. To understand this, in many cases, "が" is used when you already recognize "the part after が" as the topic and want to emphasize "the part before が" as new fact. And "は" is used when vice versa, or when you describe the whole parts as new fact, etc. "は" is more generic. And "が" or "は" is also used in the case to repeat the phrase that someone said before. The reason why [a] is strange I think is that between the former clause and the latter clause, the topic has a little changed from 金魚は...が好き to 金魚は...あまり好きじゃない, and "が" is still used without any indication about it. And the difference between [c] and [d] is like this. In [c] the emphasis is on "あまり好きじゃない" and in [d] on "かい水" and indicates it more exclusively. You can use this [d] like when giving advice to others to emphasize the importance of avoiding かい水. It might exist better explanation. But I just can explain like this way for now. Adding to the explanation above, I thought out examples of questions to get each of the answer [b] - [d] for your reference. For [b]: 金魚は たん水"が" 好きですか？　かい水"は"どうですか？ For [c]: 金魚は たん水"は" 好きですか？　かい水"は"どうですか？ For [d]: 金魚は たん水"は" 好きですか？　（また、）あまり好きでないもの"は"ありますか？ Hope this helps.