The country’s biggest water supplier announced Steve Robertson was being replaced in the top job by chairman Ian Marchant while a permanent successor was found.
Mr Robertson, who had been in the role less than three years, will leave the company at the end of June, Thames Water said.
Mr Marchant said Thames Water had seen “significant change” and Mr Robertson had put “building blocks” in place for the company’s long-term success.
“We need to continue to ensure that Thames Water is an organisation that both customers and staff feel proud of,” he said.
“We remain fully committed to our proposed business plan focused on providing industry-leading customer service through a substantial investment programme which we are determined to deliver.”
Mr Marchant said Thames Water’s executive team had to meet its “vital” responsibilities to its millions of users “each day”.
Mr Robertson said he was “proud of what we have achieved over the last two and a half years” but admitted “challenges remain”.
Thames Water is the UK’s biggest water and wastewater services provider, with more than 15 million customers across London, the Thames Valley and surrounding areas.
Earlier this year, it was among 14 firms to fail a business review by industry regulator Ofwat, which ordered Thames Water to “substantially rework and resubmit” its five-year plan.
The watchdog placed the firm under “significant scrutiny” and said it had the most to do in order to deliver lower bills and better service for customers.
Thames Water submitted new plans, which included aims to reduce combined bills by 1.3% and set more ambitious targets on reducing pollution, supply interruptions and flooding.
In January, water companies were criticised for their response to winter weather in early 2018 that caused supply interruptions to more than 200,000 customers across England and Wales.