More than 50% ADC noise using Arduino MKR Zero

Not sure where you problem is, however low level signals are inherently noisy.

For example: the first half is what one might like, however the 2nd half is what you can get.

Noise

  1. I couldn't make your link work.

  2. You mentioned the pot measurement was stable. Are the leads to the pot similar in length as the photo diode?

  3. I would put an 0.1µF capacitor at the analog input of the Arduino. However I wouldn't add this capacitor now as there seems to be some basic issue and a capacitor would likely mask such an issue.

  4. for testing I would put a delay before reading the analog inputs. 100 ms would be large enough to discount any timing issues.