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Would I be better getting a 90 gallon or 125 gallon for a reef only tank? The 90 gallon has a lot of hight so I was thinking that would be better. Any suggestions would be appreciated.
depth is definitely a good thing. Height is the last thing you want to consider since the higher it is, the harder it is for maintainance, aquascaping etc. That's one of the reasons why I custom ordered a tank that's only 20 inches high, but 20 inches deep and 60 inches long. more possibilities and flexibility in aquascaping.
A larger water surface area also aids in Oxygen exchange- healthier for your fish and corals
IMHO- I prefer the longer aspect ratios of tanks, whether it's a hex, column, or long tank. I much prefer things with a 3:1 to 5:1 ratio of length to height than the approximately 2:1 ratio of a 90 or 120. To me, the longer tanks give a more sweeping, panoramic view. In addition to that, concept3 raises a very valid point of increased surface area increasing the exchange of gases. So, in your place, I'd do a 125.
However, if it comes right down to having a fixed footprint no larger than the 90, I'd do the 120. Same footprint, larger water volume. I always try to pick the largest water volume for the tank in question. Like, right now, I want to expand my pico, but I only have space for that particular footprint. So, onto hex tanks I must go.
Basically, if comes down to weighing the pros and cons of both sizes in relation to your situation. Me, I have short arms (*my 22" poi hit my chest or armpit if I don't watch my inside planes. So, deeper tank maintenance for me, often requires looking like I'm getting ready for a wet t-shirt contest. :-\