For a projective variety X defined over a field K, there is a special class of morphisms ϕ : X → X called algebraic dynamical systems. In this paper we take K to be the function field of a smooth curve and prove that at each place v of K, subvarieties of dynamically small height are equidistributed on the associated Berkovich analytic space X an v . We carefully develop all of the arithmetic intersection theory needed to state and prove this theorem, and we present several applications on the non-Zariski density of preperiodic points and of points of small height in field extensions of bounded degree.