Electricity discharge into water
Fresh water is a pretty poor conductor of electricity, though muddy water will be a better conductor than clean drinking water.

I'll assume that there really is a problem with the pump, and it's not just some trivial leakage current.

The exposed wire inside the pump is at 240V AC, and the rock around the edge of the pit will be more-or-less 0V (ground).  So a current will flow through the water to ground.  Since it's fresh water, this won't be a very big current.  There will be a voltage gradient between the live wire and the rock.

If you stick a probe into the water at some point (either the multimeter or your hand), then it will be at some voltage between 0V and 240V.  Essentially, you're probing at some point in the middle of a resistor.

But since you only measured 0.5V, it suggests that the leakage current was actually very small.