We don’t know exactly what this kind of garden looked like since the ones from the period no longer exist. However, later Japanese gardening practices were heavily influenced by Zen philosophy, which was not yet widespread in Japan when the Sakuteiki was written. So the gardens it describes may have been somewhat different from their later incarnations. Still, it’s clear that the key feature of a stone garden — evoking water in a dry landscape — existed. Two factors influenced their evolution into their modern forms.
1. Zen teachings. The first factor was the spread of Zen thought throughout Japan. This school of Buddhism came from China and flourished in Japan from the Kamakura period to the Edo period (late 12th century to early 16th century).
2. Art forms. The second factor that led to the development of the modern-day stone garden was the influence of the bonkei and sansuiga art forms. Bonkei (tray scenery) is the practice of arranging sand, stones, and miniature plants on a tray to create a miniature replica of natural scenery
This new form also fit well with the advent of the wabi-sabi aesthetic, or the appreciation of that which is imperfect or incomplete. Stone gardens, therefore, began to be adopted beyond Zen temples as even samurai and merchants began creating their own.