A Freedom of Information Request revealed that United Lincolnshire Hospitals Trust had fines totalling £3,984,591.65 since 2015.
The figure includes sanctions for missing A&E, cancer treatment and planned operation targets.
Trust bosses said money from the fines has been reinvested in local services to help improve performance against national standards.
Under its contract with local CCGs, the organisation is fined if it fails to meet some waiting time targets but is handed money back to put into services.
Last year ULHT had £1.4 million worth of fines, £600,000 of which were reinvested.
By the end of the 2015/16, the trust had fines of £2,089,067.64 alone.
In the same year, ULHT had £1,489,180.38 in financial penalties for not meeting the four hour standard for admitting or treating patients in its emergency departments.
The trust has failed to meet the 95% target for A&E waiting times since September 2014.
ULHT said £1.6 million of the penalties in 2015/16 were put back into services.
Meanwhile since 2015, the trust ran up fines worth £946,385.98 for missing its planned operation target, which is set at 92% of patients treated within 18 weeks of a referral.
ULHT was also hit with penalties totalling £149,025.04 for missing cancer care targets.
Patients are expected to start cancer treatment within 62 days of an urgent GP referral.
But, ULHT has not met the required 85% standard since September 2014.
A spokesperson for ULHT said: “We are constantly making efforts to improve our performance against all of the NHS constitutional standards.
“This includes a cancer improvement plan in partnership with the Cancer Alliance, which helps deliver more one-stop clinics for patients and faster diagnostics than ever before.
“For urgent care we have an improvement programme which last year delivered our Pilgrim Hospital ‘Big Change’ programme, helping to speed the flow of patients through our A&E and reducing overcrowding and waiting times.
“This year we are doing similar work at Lincoln, in addition to working with primary and community care services to help streamline and improve our discharge processes.”