There's no reason to expect that the set of real points tells you the full story in an arithmetic situation. For example, can you tell that $\pi$ is transcendental but that $\sqrt{10}$ isn't from looking at their relative positions on the number line?
One thing you can do which (depending on your tastes) could count as geometric is looking at Frobenius elements.
Proposition: Let $f(x) \in \mathbb{Z}[x]$ be a monic irreducible polynomial. Suppose that for some prime $p$ not dividing the discriminant, $f$ splits into irreducible factors of degrees $d_1, d_2, ... d_k$. Then there is an element of cycle type $(d_1, d_2, ... d_k)$ in the Galois group of $f$.
Hence you can find a transposition in the Galois group (and show that the Galois group is $S_3$) by finding a prime $p$ relative to which $f$ splits as the product of a linear and an irreducible quadratic factor. (This is completely analogous to the situation over $\mathbb{R}$: one might say that complex conjugation is the "Frobenius element at infinity.")
Geometrically, instead of looking at the real points of the scheme $\text{Spec } \mathbb{Z}[x]/f(x)$, we look at points over finite fields. But from a scheme-theoretic point of view all of these points are included in the geometry of the "arithmetic curve" $\text{Spec } \mathbb{Z}[x]/f(x)$.
The Frobenius density theorem even guarantees that the converse holds: for every cycle type in the Galois group there is a prime $p$ realizing that cycle type.