So the way you're phrasing this implies that Navies were always conjoined logistically and had the same commanders as land forces before a certain series of innovations. This is not necessarily true. Certain ancient states, like Rome, tended to depend on their armies to crew fleets and lead them. However, ancient mercantile cites like Athens had dedicated naval installations, civic and logistical structures going back as far as historical accounts extend. For the most part of the ancient period, up until the early modern period, organizing the fleets as an appendage of the army or as a separate and independent entity was an option which different states choose at different times.

The Athenian Navy was organized as a separate element of the Polis from the land forces and recruited from separate social classes. Rich magnates bought warships and staffed them, landed farmers bought armor and wore it in the phalanx, landless citizens of the city (artisans and merchant sailors) served in the fleet in times of war. Shipwrights and sailors formed a significant naval and mercantile class which staffed the harbor at Piraeus and formed a significant voting bloc in the assembly. The military harbor contained expensive purpose-built ship sheds, storage for rigging and the guards needed to prevent fire, theft or sabotage when triremes wintered in Pireaus. While command arrangements were not completely separate, standard practice was to assign some generals (strategoi) to the Army and some to the fleet, while others supervised the naval base and ship commanders/owners (trierachs).

In contrast, Roman organization typically subordinated naval assets to Legions and had an 'ad hoc' method of constructing fleets as needed and placing them under the control of officers with broad experience in the Roman army. Of course, "Roman" covers a long period of time, during which various arrangements were tried, but the basic idea of a fleet as an army with some shipping under it's control might be said to be an alternative paradigm to an institutional navy. For most states with a large army, this was a more common method of organization.

These two paradigms of naval organization were both viable (until the early modern period) and employed many times in different European and Mediterranean states. Venice, Genoa, and countless other mercantile cities and small states operated a navy independant from land forces in the way Athens had. Whereas the majority of land powers in the middle ages or late antiquity operated a navy as 'an army that happens to be using some boats'. In fact the two paradigms often coexisted within the same states (including Rome) that controlled extensive territories. Habsburg monarchs dominated by Castile used the naval expertise in the Aragonese merchant cities. French kings could hire Genoa mercenary fleets to control the English Channel or their subjects could 'take the cross' effectively under command of Venetian naval leaders. Venetians or Byzantines could hire mercenaries from land oriented states.

In the Early modern period this began to change. After the Spanish Armada's defeat in 1588 it became clear that entire states could organize their Navy as a professional and permanent class on the pattern of a merchant city. The proportion of soldiers embarked declined and specialized equipment like large cannon began to dominate sea battles. Long distance voyaging put a premium on recruiting and retaining experienced seamen. Navies organized as an ad hoc support of the Army were increasingly vulnerable to well trained professional seamen backed by an extensive large scale dockyard industry, of which at least a portion (like forging large cannon and shot) was purely military. The professional, institutional Navy, had become dominant.

Sources:

Hale, John R. Lords of the Sea - The Epic Story of the Athenian Navy and the Birth of Democracy

Rodger, N.A.M. Safegard of the Sea: A Naval history of Britain