In Kent, Dartford Junction, which Network Rail says is the busiest in the county, was upgraded to improve its reliability.
A programme of station improvements was also completed at stations with no services, including reducing the stepping distance from platforms to trains at Dartford and and new LED lighting and additional customer information screens to aid journey planning were installed at Northfleet.
Buses have been running instead of trains.
The works took place during school half-term as passenger numbers are “typically lower”, Network Rail said.
The alternative was a series of weekend closures.
Follow-up works are planned for both routes, with passengers able to check how journeys will be affected on the National Rail website, or on the relevant operators’ sites.