Southern Water discovered that waste water had been flowing into the creek after reports of a overflowing manhole at Watersmeet on the foreshore last Sunday.
Work has since been carried out at the site to prevent more waste water flowing into the creek.
A spokeswoman for Southern Water said: ‘We attended a report of an overflowing manhole at Watersmeet on the foreshore in Fareham.
‘Our crew was on site immediately and following investigations, they found a small flow of waste water passing through the surface water sewer, which has been found to be the source.
‘Work began on Sunday to prevent wastewater entering into the creek as an environmental protection measure and it is necessary for this to continue until the sewers at Gosport Road and Salterns Lane junction can be rectified.
‘We are working hard to fix the problem and expect to complete the necessary works by the middle of next week. We apologise for an inconvenience caused.’