Thinking about this Manjeet, I think you need to see where the reflections on the glass are coming from when you view the fish tank from the scope position. You may then be able to mask those reflections with card.
When I am doing flash I quite often use card to prevent light falling on parts of the subject.
Is it possible to get a pic of the whole tank at minimum magnification that might give a bit of an idea of your problem ?
Don
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