Greenpeace found "yellowish foam" on the water's surface, but said an analysis of samples taken alongside Russian authorities "gave little clue".
It said possibilities included natural causes - "such as toxic phytoplankton growth, seismic or volcanic activity" - but that man-made actions could also be responsible such as "toxic waste dumping, a fuel spill or tanker accident, or military activity".
The World Wide Fund for Nature (WWF) said the pollution appeared to be caused by a highly soluble substance.