The source of the river is near Debden Green, a village near Thaxted. The source of the River Can is also nearby. The River Chelmer flows past Thaxted, south through the district of Uttlesford around the northeast of Great Dunmow. It continues flowing south-southeast into the borough of Chelmsford and on into the city of Chelmsford where the River Can flows into it. It then flows east through the borough and into the district of Maldon until it meets the River Blackwater near Maldon. It discharges into the North Sea via the Blackwater Estuary
The Chelmer and Blackwater Navigation Company was found by act of parliament in 1793. Work then commenced on constructing the navigation from Chelmsford to Colliers Reach in the tidal estuary of the River Blackwater. The work was completed in 1797. The navigation mainly followed the course of the River Chelmer from Chelmsford to Beeleigh near Maldon. From there it continued through a short cut and then followed the course of the River Blackwater to Heybridge.
According to Edward Arthur Fitch, the Fullbridge (the Chelmer river crossing at the bottom of Market Hill, Maldon ) was a shallow ford. This was before the waters of the River Blackwater were combined with the Chelmer at Beeleigh, resulting in a much greater flow of water past the Fullbridge.
In the spring of 1812 the Chelmer above the Fullbridge was straightened and many important changes were made to the bed of the river. Some of these changes are clearly visible today. For example, an island that's shown on the 1777 Chapman and Andre map of Essex was moved from the middle of the river to fill in a curve to the north near where Tesco's is today. Further upstream, near the golf course, similar earthwork is visible and, from that point to Beeleigh weir the channel appears to be a cut bypassing the original course of the river.
At Beeleigh, there was a water mill on the original course of the Chelmer. This mill operated until 1875, when it was destroyed by fire. The mill had two bays inside, where lighters were loaded with flour to be taken to the port at Maldon, about a mile downstream. There it would be loaded onto Thames sailing barges and taken to London. Part of the mill still remains and is leased by Essex County Council with the intention of restoring it.
- "The Company of Proprietors of the Chelmer and Blackwater Navigation Limited". Retrieved 2009-05-15.
- Fitch, Edward Arthur: Maldon and the River Blackwater. Gowers, 1895
- Chapman and Andre: Map of Essex. (Essex Record Office ref: D/DBy P9)
- "Maldon Archaeological and Historical Group - Beeleigh Mill". Retrieved 2009-05-15.