We investigate the critical properties of the spin-$1$ honeycomb antiferromagnet BaNi$_2$V$_2$O$_8$, both below and above the ordering temperature $T_N$ using neutron diffraction and muon spin rotation measurements. Our results characterize BaNi$_2$V$_2$O$_8$ as a two-dimensional (2D) antiferromagnet across the entire temperature range, displaying a series of crossovers from 2D Ising-like to 2D XY and then to 2D Heisenberg behavior with increasing temperature. In particular, the extracted critical exponent of the order parameter reveals a narrow temperature regime close to $T_N$, in which the system behaves as a 2D XY antiferromagnet. Above $T_N$, evidence for Berezinsky-Kosterlitz-Thouless behavior driven by vortex excitations is obtained from the scaling of the correlation length. Our experimental results are in accord with classical and quantum Monte Carlo simulations performed for microscopic magnetic model Hamiltonians for BaNi$_2$V$_2$O$_8$.