A bipolar flow junction was a conduit branch within the plasma feeds of a starship warp propulsion system. It was attached directly to the secondary warp plasma feed.
In 2374, Miles O'Brien believed the USS Rubicon had almost reached the bipolar flow junction of the USS Defiant. His uncertainty was due to the fact that he, Julian Bashir and Jadzia Dax and the runabout had shrunk down to a size small enough to fly through the Defiant, and he wasn't used to viewing the latter ship from that point of view. (DS9: "One Little Ship")