This was done in the 1970s after a scare about mosquitoes carrying encephalitis breeding in stagnant creek water (see also "Threats from Development" below).

The next 1.6 km (1.0 mi) stretch, however, a crescent shape that proceeds east to a point just west of Markham Road and which had been previously altered, has now been restored to a more natural state with gentle meanders and shallow pools.

The central branch begins at the exit of a culvert north-west of Middlefield Road and Finch Avenue East at 43°48′49″N 79°15′40″W / 43.81361°N 79.26111°W / 43.81361; -79.26111.

The branch then travels south-east under Military Trail, the first crossing point north of Lake Ontario built in the early settlement period, and Ellesmere Road.

South of Ellesmere, the branch enters Morningside Park (Toronto), where the tributary West Highland Creek joins at 43°46′27″N 79°11′57″W / 43.77417°N 79.19917°W / 43.77417; -79.19917.

It travels east through the park, under Morningside Avenue and past some of the outdoor sports facilities and the Miller Lash House of the University of Toronto Scarborough.

The valley of Highland Creek contains a number of interconnected parks which have a system of paved bike and walking paths.

As a result of these numerous channel modification projects, mostly implemented in the 1960s and 1970s, much of the creek does not follow its natural path.

This is in contrast to the nearby Rouge River, which has fewer in-stream barriers and extensive riparian and floodplain vegetation, and where a wider variety of wildlife, including some climax forest species, can be found.

A 2005 excavation by the Toronto and Region Conservation Authority near the mouth of Highland Creek found evidence of a Late Woodland or Early Archaic site, thought to have been a place of tool manufacture.

During the late 1940s and early 1950s, a new town plan developed in the valley between Kingston Road and the eastern crossing of Lawrence Avenue.

Opposite the former village of Highland Creek is West Hill, named for its position on the tablelands above the valley.