The magnetic properties of the two-dimensional, S=1 honeycomb antiferromagnet BaNi$_2$V$_2$O$_8$ have been comprehensively studied using DC susceptibility measurements and inelastic neutron scattering techniques. The magnetic excitation spectrum is found to be dispersionless within experimental resolution between the honeycomb layers, while it disperses strongly within the honeycomb plane where it consists of two gapped spin-wave modes. The magnetic excitations are compared to linear spin-wave theory allowing the Hamiltonian to be determined. The first- and second-neighbour magnetic exchange interactions are antiferromagnetic and lie within the ranges 10.90meV$le$J$_n$$le$13.35 meV and 0.85meV$le$J$_{nn}$$le$1.65 meV respectively. The interplane coupling J$_{out}$ is four orders of magnitude weaker than the intraplane interactions, confirming the highly two-dimensional magnetic behaviour of this compound. The sizes of the energy gaps are used to extract the magnetic anisotropies and reveal substantial easy-plane anisotropy and a very weak in-plane easy-axis anisotropy. Together these results reveal that BaNi$_2$V$_2$O$_8$ is a candidate compound for the investigation of vortex excitations and Berezinsky-Kosterliz-Thouless phenomenona.