The origins of the Shadowy Seas are not described, and in principle they might have existed since the making of the world. Given that their shadows functioned as part of the defences of the Blessed Realm, however, they seem more likely to have been put in place by the Valar as part of the protection of their land in the West. This would presumably have been done soon after the Valar travelled there from Middle-earth in the very distant past, and indeed we know that the Valar took thought to their defence at this time, raising the mountains of the Pelóri along their eastern coasts. The creation of the Shadowy Seas would seem to fit this timeline, too, but they are not specifically mentioned in accounts of the period.

In Namárie, Galadriel's song of farewell to the Company of the Ring, there's a reference to Varda causing deep shadows to appear, so that '...all paths are drowned deep in shadow...' and '...darkness lies on the foaming waves...' (The Fellowship of the Ring II 8, Farewell to Lórien). This certainly sounds as though it describes the creation of the Shadowy Seas, and in his commentary to these words in The Road Goes Ever On, Tolkien explicitly describes Varda's actions as following the Darkening of Valinor and Melkor's escape to Middle-earth.

Galadriel's song would seem to place the making of the Shadowy Seas long after the arrival of the Valar in Aman, but matters are confused by a mention of the Shadowy Seas early in The Silmarillion, where they are named as existing in a time long before the Darkening of Valinor (indeed, in a passage in that directly describes the shining Light of the Trees). From this, it seems that the Shadowy Seas must have existed in some form while the Two Trees still shone, but perhaps we can take Galadriel's words as implying that their shadows only became impassably dark after the Two Trees had been destroyed.

The arrangement of the Shadowy Seas and the Enchanted Isles shown here is based on an early sketch map reproduced in volume IV of The History of Middle-earth. Some of the geography on this map is rather different from the form it would later take, and so this map is certainly not definitive, but no more recent maps of this region exist.