I know there's breeding Bagon with the Horsea line and using the dexnav(for ORAS), but are there other ways(specifically including chain breeding)?
There are a few other mons you can breed with to get Hydro Pump, namely Milotic, Gyrados, and the Dragalge line. Each of these Pokemon get Hydro Pump by level up however.
Source: https://m.bulbapedia.bulbagarden.net/wiki/Bagon_(Pokemon)