On Thursday a tanker arrived on site and worked for two days to remove as much of the polluted material as possible.
This was able to happen after a contractor was brought in to support the clean-up, installing and renewing booms in the watercourse focused on containing the contamination.
The council has said that further remedial work is due to take place including the removal of contaminated material from manholes, enabling SEPA to undertake camera investigations.
Sharon Saunders, Head of Communities, East Lothian Council, said: “This has been a very concerning pollution incident and we are grateful to local residents for their understanding and support.
“Officers have been working hard since last Friday to contain the pollution with work continuing to take place, supported by our contractor, to progress clean-up work.
“Work is likely to continue in the days ahead and we’ll continue to closely monitor the situation, with a sharp focus on protecting the natural environment.”
Progress assessments will be made each day to inform decisions on how to further tackle the problem, which will include the tanker being deployed again if necessary.
The extent of discoloured water has reportedly reduced over recent days but the council has pointed out that locals may still notice some residual material as they expect it will take some time to dissipate.
Residents have been asked to stay away from the areas where contractors and officers are working to ensure investigations and clean-up can continue safely.
Chris Dailly, SEPA's Head of Environmental Improvement, said: “We know this pollution incident has been very concerning for local communities and are very grateful to people for their information, support and understanding during this incident.
“SEPA officers are pursuing a number of lines of enquiry in what is a complex incident and continue to provide advice and support to East Lothian Council.
“We will provide as much information as we can, within the restrictions of a live investigation. What is important is that our investigation is thorough, with our work done to a high evidential standard.”