A GFCI extension cord will provide the same level of protection as a wall mounted GFCI.

You may have nuisance tripping of the GFCI when the pump starts and stops though.

The magnetic field build up and collapse in the motor as it starts and stops can cause enough current on the ground, or current mismatch on the hot and neutral, to trip the GFCI device.
The current sensitivity is about 0.006 amps, 6 thousandths of an amp.

I will confirm that Brick knows what he is talking about.
The GFCI will protect the pump, the dog, etc, that is plugged into it. They pretty much mandate the cords for hair dryers and things that people use near a sink/tub have them inline as well.

Be sure to test your GFCI now and again.

Thanks for the advice!