vvarrior:
I am using 3.3v instead of 5v because I need to shut off the sensor. I am testing the electrical conductivity of water, as well as pH. Testing conductivity throws off the pH reading.
That's normal. Ground loops. Putting caps in your EC probe connection can help a lot (what probe/sensor are you using for this?) as it stops DC currents. With my EC probe in the water hose and the pH probe in the reservoir I don't have any such issues; haven't yet tried to put the EC probe in the reservoir.
And just to clarify, I want to use 3.3/1024 instead of 1023?
No - 5/1024. But you're probably losing a lot of precision here.
First of all: find the ACTUAL voltage range of your pH probe output. There's probably an offset applied, but the output of a pH probe is only about 60 mV/pH point. That's 12 ADC points for 1 pH point shift. You want this offset to be as low as possible, so the highest pH value you measure gives an output close to 0V, and the lowest pH gives an output of <1V.
This way you can use the internal 1.1V reference. Two advantages: much more stable reference voltage (independent from fluctuations in Vcc; your pH probe produces an absolute voltage anyway), and a much better range (1 pH point is now 60 ADC points).