Network Rail said the clay soil underneath the c2c lines, which run train services connecting east London and Essex, has shrunk following the driest spring since 1974.
This has caused the tracks to drop in places and become uneven, it said.
Speed restrictions will be applied from Monday (August 18).
Trains will operate at slower speeds, leading to a few minutes’ delay in some journeys.
A small number of services will start or terminate early or not stop at some stations, Network Rail said.
Journey planners will be updated with the amended timetable by the end of this week.
Passengers are advised to check c2c-online.co.uk or nationalrail.co.uk before travelling.
Simon Milburn, infrastructure director for Network Rail Anglia, said: “We are really sorry for the disruption to passengers from the timetable alterations, but we need to keep everyone moving safely.
“Our teams are working together to keep running the best possible service for passengers, even with the significant challenges we face with clay soil following prolonged dry spells.
“Thank you to everyone for bearing with us – and please do check before you travel, particularly if you’re used to getting the same time train every day.”
Network Rail aims to improve the condition of the track using machines called tampers and stoneblowers.
These machines will correct the level of the track and create a solid foundation to ensure smooth train operations.
In the last year, Network Rail has dropped 12,600 tonnes of ballast across the route in a bid to minimise the effects of clay shrinkage.
But it said the exceptionally dry spring this year has made it impossible to eliminate track issues.
The combination of engineering work, speed restrictions and service alterations from Monday is intended to prevent more disruptive reductions and changes to timetables and calling patterns.
The alterations are expected to be in place for between two and three months, and planned weeknight and weekend engineering work will continue.
Stuart Browning, operations and safety director for c2c, said: “We are working closely with our Network Rail colleagues to ensure the safe running of our services for customers.
“We are sorry there will be some disruption due to these timetable alterations.
“We are hopeful these small amendments will not inconvenience our customers’ journeys but we would urge customers to check before they travel.”
