Vassilis Sfakianopoulos of clean-up group Save Your Hood said the dump on the riverbank included nappies and medical records from one of the capital's main hospitals, in addition to rubbish from at least two nearby businesses, a foreign airline and a swanky central Athens restaurant.
"It seems (the waste) was gathered somewhere else before it was brought to this location," Sfakianopoulos, the group's founder and director, told AFP.
"This must be investigated," he said.
Save Your Hood had recently carried out clean-up operations elsewhere along Kifissos, so seeing the new dump was a "gut punch", Sfakianopoulos said.
He added that according to locals in the municipality of Acharnes, the illegal fly-tipping operation was probably carried out under cover of darkness months ago.
Illegal waste disposal is a long-running problem in Greece that has resulted in millions of euros (dollars) in fines from the European Union.
The hospital said it had assigned its records removal to a private contractor and would cooperate with any investigation, according to daily newspaper Kathimerini, which broke the story on Tuesday.
Kifissos, the main river crossing Athens, partly runs beneath a major motorway.
Although mostly dry in summer, it is a habitual flood risk to nearby communities at times of heavy rainfall.
The greater Athens regional authority said in a statement to AFP it had removed over 45,000 cubic metres (1.6 million cubic feet) of waste from the riverbed over the past months.
It said it had alerted police and justice officials to investigate.
The local council in Acharnes was approached for comment.
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