The Gemara earlier that answered "Safek d'Divreihem l'Hakel," as Tosfos there (DH "Ibais Aima") points out, was quite a Chidush (as the leniency was actually only because of Eiruv, and would not be said if it was a different Din d'Rabanan). It was also an alternative answer. Additionally, the case of the clouds is that we are unsure whether there is a new cloud in the sky or an old cloud.

However, in our case there are clearly two sides of water, with the Metzius being that water from one side rushes into the other side all the time. It therefore is not as appropriate to apply a special leniency of an Eiruv for which we will rule Safek d'Rabanan l'Hakel.

Kol Tuv

Yaakov Montrose