In this case, is, ea, id is a demonstrative pronoun (like hic, haec, hoc; ille, illa, illud; etc.).
Allen & Greenough §297 says the following about is, ea, id:
Is is a weaker demonstrative than the others and is especially common as a personal pronoun. It does not denote any special object, but refers to one just mentioned, or to be afterwards explained by a relative. Often it is merely a correlative to the relative quī:—
vēnit mihi obviam tuus puer, is mihi litterās abs tē reddidit (Att. 2.1.1), your boy met me, he delivered to me a letter from you.
eum cōnsulem quī nōn dubitet (Cat. 4.24), a consul who will not hesitate.
Your sample sentence demonstrates this correlation with a relative pronoun. You could translate as:
The [or: "that"] place by which a river flows into the sea is called the ostium [doorway] or os [mouth] of the river.