I understand that cations (positive ions) can not pass these channels because of the presence of positively charged amino acids at the center of their pores, so that they repulse from them and can not pass...
But what about negative ions and other uncharged molecules? What makes these channels highly selective to water ?
It appears that the positive residues responsible for filtering out cations may also coordinate anions and trap them[1].
For the aquaporin-1 the narrowest opening is only 2.8Å wide[2], which does not leave space for any anions, except for the hydroxide-ion
However, there are other aquaporins that are able transport anions and other compounds[3], so the question really depends on which aquaporin you are discussing.
[1] http://www.ncbi.nlm.nih.gov/pubmed/15951380
[2] http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2658677/
[3] http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4150397/
Bjarte is correct. It may depend slightly on the aquaporin isoform. However, one conserved feature in all aquaporins is the NPA filter. This is an Asn-Pro-Ala motif where the Asn is facing the channel lining. This motif appears twice in the protein and the Asn are located sequentially in the channel lining. The side chains of these residues are responsible for creating a positive dipole moment that flips water molecules, preventing them to go back in either direction, and prevents the passage of charged species.