In Song of Solomon 5:12 the young woman compared his eyes to doves besides streams of water, sitting beside a full pool. In the Song, linking eyes with abundant moisture is a way of describing their beauty. So, here he too says her eyes are pools in Heshbon, by the gate of Bath-rabbim.
It is not clear, historically, which pools he has in mind, but the comparison suggests depth and the reflection of light; the lover could, as it were, drown in her eyes.1
4 Your neck is like an ivory tower. Your eyes are pools in Heshbon, by the gate of Bath-rabbim. Your nose is like a tower of Lebanon, which looks toward Damascus.