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Single junction probes put the reference electrode in direct contact with aquarium water. Over time, the junction will slowly leak aquarium water into the electrolyte which changes the accuracy of the probe and requires more frequent calibrations.
Double junction probes place a second vessel inside the main electrolyte with a second internal junction. The means that even when the aquarium water eventually begins to make its way in the first compartment, it still has to go through the second junction to contaminate the electrolyte surrounding the reference electrode.