It could be days before the cause of the large foamy discharge spotted in the Waikato River for a second day is revealed.

Waikato Regional Council is blaming this morning's heavy rain for flushing additional amounts of the unknown detergent-like substance into the river from a stormwater pipe situated at the northern end of the St Andrews golf course.

Members of the public first alerted the council about the foam entering the river on Sunday morning.

Waikato Regional Council is still waiting on test results to confirm what the substance is and has been warned it could take several days.

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"Because the detergent-like substance remains unidentified, it is not known what – if any – environmental impact it may have," a council spokesperson said.

The regional council has contacted businesses between St Andrews and Horotiu that are drawing water immediately to exercise caution and, if concerned, to use alternative water sources until test results are available.

The public is also being urged to be cautious about entering the water immediately downstream too.

The foam has been spotted floating along the river from the St Andrews stormwater pipe to Pukete before dispersing.

While the tests are being carried out, the regional council is making its own inquiries and Hamilton City Council staff are also checking their stormwater network to see if they can identify a possible source for the discharge.