Inner Seas is a concept that refers to different bodies of water in different Ages of Arda.
Inner Seas in the earliest times of Arda
The Inner Seas in the very beginning of Arda were Belegaer and the East Sea, the two oceans between the two outer continents (Aman in the West and the Land of the Sun in the East), and Middle-earth proper, contrary to the Outer Sea that extended from the edges to the nether side of Arda.
In the Ambarkanta the Inner Seas, or "the ancient seas", are described as laying "in troughs" between the central continent and the western and eastern lands, and their waters only spilled into the chasm in north and south, where they had no shores.
Inner seas in the Second Age
When the Dúnedain could not go very far to the West from Númenor because of the Ban of the Valar they are told to have sailed eastward from North to South and they "came even into the inner seas, and sailed about Middle-earth and glimpsed from their high prows the Gates of Morning in the East".
These "inner seas" were reached from the Belegaer and therefore must have referred to something quite else than the great Inner Seas of the beginning of days.
The answer may be found from the Ambarkanta Map V which depicts the geography of Arda after the destruction of the Lamps of the Valar: in the places where the Lamps stood, had been formed two great bodies of water, the "Inland Sea" or the Sea of Helcar in the North, and the "East Sea" in the South. Especially the East Sea, to the south of which was the Dark Land, offered a route from the Belegaer to the great eastern ocean – also named as the East Sea, in the Ambarkanta Map IV.
Note that the "East Sea" of the Ambarkanta Map V was named as "Inner Seas" by Karen Wynn Fonstad in the map that describes the voyages of the Dúnedain in the Second Age, obviously based on the mention in the Akallabêth and disregarding the name Tolkien himself gave to the sea.
- J.R.R. Tolkien, Christopher Tolkien (ed.), The Silmarillion, "Quenta Silmarillion: Of the Beginning of Days"
- J.R.R. Tolkien, Christopher Tolkien (ed.), The Shaping of Middle-earth, "V. The Ambarkanta", p. 238.
- J.R.R. Tolkien, Christopher Tolkien (ed.), The Silmarillion, "Akallabêth: The Downfall of Númenor"
- J.R.R. Tolkien, Christopher Tolkien (ed.), The Shaping of Middle-earth, "V. The Ambarkanta", p. 251.
- J.R.R. Tolkien, Christopher Tolkien (ed.), The Shaping of Middle-earth, "V. The Ambarkanta", p. 249.
- Karen Wynn Fonstad, Atlas of Middle-earth, Revised Edition, p. 45.