A setting tool and bridge plug that are run-in-hole on wireline through a core bit while drill rods are in place can be used to plug a borehole. A setting tool can be sized to have a same or smaller diameter as a drill rod. A bridge plug can have a run-in configuration of a diameter that is smaller than an inner diameter of a core bit. The bridge plug can have a set configuration that can respond to the setting tool pulling uphole. The bridge plug can be positioned below a drill bit of the drill rod in the set configuration, and the diameter of the bridge plug in the set configuration can be greater than the diameter of the drill rod.