Not all of it was historically part of Croatia except for some brief moments. The actual borders of Hercegovina , especially in the western , parts have changed as they were never official. Nowadays , Livno , Tomislavgrad , Suica and basically the whole Herceg-Bosanski kanton is considered 'Hercegovina' rather than Bosnia yet this region was never historically Herzegovina but has indeed been part of Croatia or closely aligned with Croatia/Dalmatia. When someone says Bosna I Hercegovina its sort of the 'I' between BiH or what we Croats just called the heart of Herceg Bosna. Culturally it's closer to Herzegovina than the rest of Bosnia with ganga , gusle , and vino . It's believed historically that the Neretva was a 'border' between the East and Western Catholic church ( eastern is Orthodox) and pretty much is that way today while northern Herzegovina is mostly Muslim. A couple centuries ago with the rise of nationalism Catholics became Croats , Orthodox became Serbs , and Muslims eventually became their own Bosniaks. Historically this region was occupied by Slavs before the Croats even arrived. Slavs invaded the Balkans with the Avars and settled in these regions. They were called Neretljani who were like Slavic pirates. They drove out the Illyrian and Latin residents until the Croats arrived. The Croats made the Neretljani and the latins pay tribute and essentially made them vassals. When Croatia became a kingdom Petar Kresimir IV annexed western Herzegovina and made the Neretljani part of his fleet. From this point on there has always been a connection between Croatia ( especially slavic Dalmatia) and SW BiH and its seen in the common culture between Dalmatinska Zagora and Zapadna Hercegovina. The land on the western side of the Neretva was almost purely Catholic as well and Croatdom was a natural consequence when Croatian nationalists began to dominate our culture.
Hope that helps .