The river in its natural state used to flow openly from the northern parts of Moscow to the south across the very centre of the city.

The moat did not stop foreign invasions but slowed development of territories west of the Kremlin; initially, the city grew eastward, into Red Square and Kitay-gorod.

When Muscovites began settling on the western side, territories around the Neglinnaya remained vacant due to frequent flooding.

A new masonry canal, one sazhen (2.13 m) wide, was laid parallel to the Neglinnaya; after diverting water into the channel, builders filled the old river bed with earth.

In 1966, the city built a second arm for the Neglinnaya River (length: 1 km, width: 4 m), cutting the path under Zaryadye.