Automating Lights/Feeder/Pump for Aquaponics using Arduino

Chagrin:
Using the moisture sensor in a way that would allow it to get repeatedly wet would (assumedly) result in it getting scummy and failing to read correctly. I don't think it's a good long-term solution.

With respect to what Arduino you need your primary requirement is that you have enough IO pins for your project as it certainly isn't a processor-intensive task. There's 14 digital and 8 analog on a typical board. A Mega will give you more of both or you can add on an IO board like the Mux Shield. Whether or not you use multiple boards really depends on whatever you think is practical -- taking into account that you might need to create communication between them which could create headaches in itself depending on the distance you need to cover.

If I'm simply setting:

An Archimedes-Screw on a servo motor set to spin for 1 second and then shut off for 4 hours.

Thats what? a servo attached to maybe 2 pins? If that?

electronic PH tester to check for PH drift and changes once per hour and report to a Linux PC.

I have no idea how I'll wire an electronic PH tester to an arduino....Still, probably not the best idea to keep this around. I may have to just drop features until I get better equipment.

the room lights to allow for the grower to see should be activated, simple t5 tubes (aprox. amount of tubes: 2-4)

I'm thinking I'm going to drop this, as if this guy is too lasy to hit a light switch I just dont know anymore...

a moisture content sensor to detect overflow would not be getting wet often, if it did then my system would be an utter failure, as a matter of fact, they should remain dry unless a freak incident occurs and the main draining area get clogged.

I'm thinking one board will do, with control over a servo, and moisture sensing. I may very well pair off the T5 tubes to a simple light switch, I mean really I dont think it's needed.