We study three-dimensional gauge theories based on orthogonal groups. Depending on the global form of the group these theories admit discrete $\theta$-parameters, which control the weights in the sum over topologically distinct gauge bundles. We derive level-rank duality for these topological field theories. Our results may also be viewed as level-rank duality for $SO(N)_{K}$ Chern-Simons theory in the presence of background fields for discrete global symmetries. In particular, we include the required counterterms and analysis of the anomalies. We couple our theories to charged matter and determine how these counterterms are shifted by integrating out massive fermions. By gauging discrete global symmetries we derive new boson-fermi...