Let $\Gamma \subset \mathrm{PU}(1,n)$ be a lattice and $S_\Gamma$ be the associated ball quotient. We prove that, if $S_\Gamma$ contains infinitely many maximal complex totally geodesic subvarieties, then $\Gamma$ is arithmetic. We also prove an Ax--Schanuel Conjecture for $S_\Gamma$, similar to the one recently proven by Mok, Pila and Tsimerman. One of the main ingredients in the proofs is to realise $S_\Gamma$ inside a period domain for polarised integral variations of Hodge structure and interpret totally geodesic subvarieties as unlikely intersections.