The substance which has definite composition with definite physical and chemical properties is said to be pure substance. These substances are not separated by the different physical techniques such as filtration, distillation, evaporation etc.
The clear water pumped from a deep aquifer is a pure substance because water is a pure compound which consist of constant single type of atoms or group of atoms and water has specific value of boiling and melting point. Water is also not separated into units or constituents by physical technique.
Hence, clear water pumped from a deep aquifer is a pure substance.
As pure substances are substances that are formed directly by elements and water is directly formed by the union of two elements which is Oxygen and hydrogen, H2O is the formula and that is a pure substance as it is conformed mainly by only these two elements, so the question would be Yes, clear water pumped from a deep aquifer is a pure substance.
In a physical change the appearance or form of the matter changes but the kind of matter in the substance does not. However in a chemical change, the kind of matter changes and at least one new substance with new properties is formed.