The Environment Agency says the risk of pollution is now a major problem for hundreds of people returning to their flood-hit homes.
People in Lewes spent yesterday mopping up after the deluge that swept across the region.
A clearer picture of the extent of the damage, likely to become the most costly natural disaster the South has seen, is starting to emerge.
People have returned to find belongings ruined, sentimental items washed away and pets killed. Farmers have reported losing livestock.
As weather experts forecast more heavy rain early today, environmental protection teams were checking sewage pumping stations, farms and chemical and oil stores, all possible sources of contamination.
There were further warnings that electricity supplies might still be live despite the destruction.
Several firefighters received minor shocks while pumping water from properties.
Environment Agency spokeswoman Jo Warburton said: "A list of priority pollution sources has been drawn up and we will press those responsible for their maintenance to rectify the problems.
"All rivers affected are being tested for chemical and pesticide contamination and the agency is also in close liaison with Southern Water over supplies where drinking water intakes may be at risk.
"The agency is also concerned that sewage overflowing from flood-damaged pumping stations will cause additional river pollution.
"Ensuring this problem is rectified quickly by water companies and others is one of the agency's top priorities."
Agency staff are bracing themselves after receiving a severe weather warning for Sussex and the South East today.
The Met Office predicts nearly 2in of rain will fall in parts of the South East by midnight.
Environment Agency crews are now regularly checking culverts and sluices in waterways near the rivers Ouse and Uck to ensure they are clear of rubbish.
Rupert Clubb, flood defence manager for Sussex, said: "Rubbish has flowed down the streams which could block waterways, causing a dam effect.
"It is vital we keep clearing it away, otherwise it could cause huge problems."
Rail services returned to normal today but operators were keeping a wary eye on the weather.
Trains between Haywards Heath and Brighton were delayed by up to an hour this morning due to flooding in Clayton Tunnel but services returned to normal by mid morning.
Workmen made emergency repairs at the weekend to track at Cooksbridge, near Lewes, and Etchingham, near Hastings, where ballast under rails had been washed away.
Lewes station, where flood water almost reached platforms last week, was back to normal.
A Connex spokesman said: "It is raining heavily again today but so far everything is going to plan."
Comments: Our rules
We want our comments to be a lively and valuable part of our community - a place where readers can debate and engage with the most important local issues. The ability to comment on our stories is a privilege, not a right, however, and that privilege may be withdrawn if it is abused or misused.
Please report any comments that break our rules.
Read the rules hereComments are closed on this article