  In this paper, we study strongly quasiconvex subgroups in a finitely
generated $3$--manifold group $\pi_1(M)$. We prove that if $M$ is a compact,
orientable $3$--manifold that does not have a summand supporting the Sol
geometry in its sphere-disc decomposition then a finitely generated subgroup $H
\le \pi_1(M)$ has finite height if and only if $H$ is strongly quasiconvex. On
the other hand, if $M$ has a summand supporting the Sol geometry in its
sphere-disc decomposition then $\pi_1(M)$ contains finitely generated, finite
height subgroups which are not strongly quasiconvex. We also characterize
strongly quasiconvex subgroups of graph manifold groups by using their finite
height, their Morse elements, and their actions on the Bass-Serre tree of
$\pi_1(M)$. This result strengthens analogous results in right-angled Artin
groups and mapping class groups. Finally, we characterize hyperbolic strongly
quasiconvex subgroups of a finitely generated $3$--manifold group $\pi_1(M)$ by
using their undistortedness property and their Morse elements.
