The creek formed a series of marshy ponds on the floodplain, with extensive salt water marshes near its entry to the Yarra river known as Batman's lagoon.
In the 1890s the lower Moonee Ponds Creek was widened for use as a canal for barges carrying coal to the North Melbourne Locomotive Depot.
In 1950s and 1960s the Melbourne and Metropolitan Board of Works realigned and concreted the creek from Strathmore to Flemington Road, in an attempt to stop periodic flooding.
Moving the confluence with the Yarra River about 600 metres upstream, the creek mouth once located at the east end of Appleton Dock was removed, with a new watercourse dug leading directly south parallel with the Bolte Bridge approach spans.
[4] While realigning waterways is not a preferred option for Melbourne Water, the work was permitted as previous modifications had left the creek lacking a "true remaining 'natural' alignment" in the area.
Recent habitat conservation work has resulted in some wildlife returning to the creek, including the pobblebonk frog around the Strathmore Secondary College, and nankeen night heron in the upper catchment.