Scorpio and Aquarius are very strong together and individually. But as a pairing, their strengths don't necessarily work well together. In astrology, they are both fixed signs. Fixed means the quality of hanging in, of being strong, of being opinionated, of being loyal.
But Scorpio is fixed in its emotions. It's fixed in its need to control and to have a life that is safe in which Scorpio doesn't feel vulnerable. Whereas Aquarius is fixed in its need to be independent, to think independently, to experience life outwardly, to go out and have new adventures, and especially not to be controlled, to be highly individualistic. Aquarius is known as the one who marches to a different drummer.
So we have these two energies of two very stubborn people, but stubborn about different things. What they do have in common is that they can come together in the early parts of a relationship and be very experimental as far as sex and exploring each other's minds, passions, and bodies. That works for a while, but essentially Aquarius is the lone wolf. Scorpio, too, being a lone wolf, but it's a lone wolf that wants another partner. Wants a wolf that is a partner to have the other lone wolf, and together you explore the wilderness, and together you will be together always.
It's hard to explain two lone wolves with different agendas, but that's exactly what Scorpio and Aquarius are, so eventually they will part and sometimes not very easily.