The Great Eastern Railway Act of 1862 was a scheme which merged most of the railway operators in East Anglia, the act also authorised the construction of the lines between Sudbury to Melford, Melford to Clare, Haverhill and Shelford and Melford to Bury St Edmunds. Construction of the line began at Shelford and continued to the new GER station at Haverhill, a connecting line to the CV&HR was also constructed. This section of the line opened on the 1st June 1865. There were initially 3 trains per day both ways on this section of the line.

The sections between Haverhill and Sudbury as well as Melford to Bury opened on the 9th August 1865. The opening of the extension required a new station at Sudbury, this consisted of two platforms on a curve to the west of the original station and eventually some fine station buildings. The original station remained as a goods station.

At Haverhill once the new station opened most passenger trains on the Colne Valley and Halstead Railway operated to and from the GER station to allow passengers to make onward connections to Cambridge rather than their own station which was then only used for freight and first and last trains of the day.
Abington was renamed Pampisford on 1st May 1873 and Melford was renamed Long Melford on 1st February 1884. A new, larger station was built at Chappel which opened in 1880.

By 1890 there were six trains a day between Marks Tey and Sudbury (weekdays) and three on Sundays, there were five services to Bury St Edmunds and four between Cambridge and Sudbury. The line was also well used by many different freight trains.
On the 1st July 1898 the Great Eastern Railway received Royal Assent to purchase the line from the CSVS&HR who they were leasing the line from. At this point the original Stour Valley Railway ceased to exist.

For many years after this date the Stour and Colne Valley Lines continued to do well. Of note the only station which had not attracted enough traffic to justify its existence was Bury East Gate, this station closed on 1st May 1909.
Summer 1914 and seven trains operated daily between Marks Tey and Sudbury, with four of these being through services to/from London. The First World War did little stop the success of the lines.

On the 1st October 1914 Chappel station was renamed "Chappel and Wakes Colne"

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