Hello.  In theory, electrical conductivity should not be affected by whether the water is flowing or not.  Conductivity meters do not change the character of the water as the measurement is taken, since the meter measures transmission of an electrical charge.  In practice, more reliable measurements arise when the water is moving at least a little bit, but in standing water, or samples, moving the probe even a little is generally enough.  So I wouldn't be concerned about comparing measurements from standing vs. still water.