Just from what I've found online for you it might have been cause you were taking him out of the water at night some aquatic turtles depending on species sleep in the water coming up for air when needed and going back to sleep or they bury themselves in mud or sand underwater some do sleep half...
Reptiles are really good at masking if they're ill so he probably wasn't good 3 days ago you just couldn't tell at that time it was most likely at the time he stopped eating when he fell ill maybe even before. It sounds like your setup was an outside pond instead of a tank inside but maybe not...