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The Gemara sees this as a proof that the nisukh ha-mayim was done in the morning, since the people were all carrying their etrogim. The background to this story involves the different sects that lived during the second Temple period and their approaches to the Oral Law taught by the Sages. Many of the kohanim were Tzedukim, who did not accept the traditions of the Sages. Unlike nisukh ha-yayin – the wine libation – which is clearly written in the Torah, the nisukh ha-mayim – the water libation – was a tradition handed down from Moshe on Mount Sinai, and it was not accepted by the Tzedukim.
The particular story referred to in our Gemara, is described in great length in Josephus. According to him, the individual who poured the water on his feet rather than on the altar was a Hasmonean king, Alexander Yannai, who rejected the teaching of the Sages. After the people – who supported the interpretation of the Sages – pelted him with etrogim, the king summoned the non-Jewish guard, and they killed many of the people who were on the Temple grounds.