In a continuum dislocation dynamics formulation by Xia and El-Azab [1], dislocations are represented by a set of vector density fields, one per crystallographic slip systems. The space-time evolution of these densities is obtained by solving a set of dislocation transport equations coupled with crystal mechanics. Here, we present an approach for incorporating dislocation annihilation and junction reactions into the dislocation transport equations. These reactions consume dislocations and result in nothing as in the annihilation reactions, or produce new dislocations of different types as in the case of junction reactions. Collinear annihilation, glissile junctions, and sessile junctions are particularly emphasized here. A generalized energy-based criterion for junction reactions is established in terms of the dislocation density and Burgers vectors of the reacting species, and the reaction rate terms for junction reactions are formulated in terms of the dislocation densities. In order to illustrate how the dislocation network changes as a result of junction formation and annihilation in a continuum dislocation dynamics setting, we present some numerical examples focusing on the reactions processes themselves. The results show that our modeling approach is able to capture the respective dislocation network changes associated with dislocation reactions: dislocations of opposite line directions encountering each other on collinear slip systems annihilate to connect the dislocations on the two slip systems, glissile junctions form on new slip system behave like Frank-Read sources, and sessile junctions form and expand along the intersection of the slip planes of the reacting dislocation species. A collective-dynamics test showing the frequency of occurrence of junctions of different types relative to each other is also presented.