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Its mother is a Wartortle that knows Waterfall, Aura Sphere, Dragon Pulse, and Water Gun. The father is a Blastoise that knows Hydro Pump, Earthquake, Ice Beam, and Surf. How will I know what move/moves their baby Squirtle will inherit? Is there a 50/50 chance of it getting Aura Sphere and Dragon Pulse because that's what I want it to know the most.

Or should I replace the Blastoise with a Ditto? Will it make a difference?

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Generally the father passes down any moves to the baby Pokemon. But only if it's in the Breeding list provided here under Egg Moves.

This link to Bulbapedia can tell you more on passing moves down, and more on breeding in general.

Bulbapedia Breeding: Passing down moves

In Gen 6 However the breeding mechanics changed and now either parent can pass down an egg move if it's on the baby's egg move learn list. So Aura Sphere and Dragon Pulse would both be passed down from the mother. This is Gen 6 only however.

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So Aura Sphere and Dragon Pulse will be absolutely passed down?
"If either parent (only the father prior to Generation VI) knows any specific Egg moves that the baby can learn, the baby will inherit the move."
-Bulbapedia

Yes, your Squirtle will have Aura Sphere and Dragon Pulse if you're breeding in Gen 6