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The PE Branch of the SA weather service reports that 25 millimetres of rain fell at the airport during Sunday's storm.
Third Avenue Dip in Newton Park measured 43 millimetres of rain.
It was closed to traffic earlier on Monday but has since been reopened.
Coega measured 37 millimetres and Uitenhage 13.
In other parts of the Eastern Cape, Joubertina measured 28 millimetres, East London 34, Storms River 23, Barkley East 21 and Aliwal North 28.