David Black, the chief executive of Ofwat, said the latest fines were a result of a "clear-cut case where Thames Water has let down its customers and failed to protect the environment".
"Our investigation has uncovered a series of failures by the company to build, maintain and operate adequate infrastructure to meet its obligations," he added.
"The company also failed to come up with an acceptable redress package that would have benefited the environment."
Thames Water is currently in "cash lock up" and no further dividend payments can be paid without approval from Ofwat.
The company had expected to run out of cash completely by mid-April before it secured a rescue loan, and the government has been on standby to put Thames into special administration.
Regardless of what happens to the company in the future, water supplies and waste services to households would continue as normal.
Ofwat said the penalties "will be paid by the company and its investors, and not by customers".
The money from the fines will ultimately go to the Treasury, but no firm decision has been made about what it will be used for.
The regulator said the March 2024 payout was funded through a tax break and that it will now make the company pay the tax to "claw back the value" of it.
In April, water bills for households in England and Wales rose by £10 per month on average, although costs vary depending on suppliers - Thames customer bills have gone up from £488 to £639 a year.
Ofwat proposed the £104m fine in August last year, but confirmed the penalty, and the additional £18.2m fine on Wednesday.