How long has it been in the system?
We just bought a lime tree, and it says on the instructions that...
1. The leaves go yellow if there is too much water.
2. The leaves go yellow if there is not enough water.
I realise that's not helpful or anything 
But yours looks pretty healthy to me. A lot of instructions for plant growth are for optimum growing conditions, but I grew a stack of capsicum over winter this year in anything but optimum conditions. Probably just 20% less than I might have if things were "just right".
With things like herbs and lemon grass etc, I've always found that there is plenty enough for a domestic kitchen, even when it's grown in less than idea conditions.
For example, I suspect the ideal conditions for rosemary is a K-mart carpark, but mine goes crazy in my aquaponics system.Those are two very different environments, but it does just fine in both. I'm pretty sure the instructions for rosemary say not to over water it. It's a hardy, can-do kind of plant, but mine is in a constant flood growbed.
If it hasn't been there for long, I would leave it and see if it settles down.
I think TCLynx's system has trees, so it might be worth a read.
But keep in mind I have no idea what I'm talking about. I've never grown a tree in aquaponics. It's just that everything else seems to do just fine.
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