Two-dimensional covalent organic frameworks (2D-COFs) have been of increasing interest in the past decade due to their potentially ordered porous structures. One of the most common routes to these polymers relies on Schiff-base chemistry, i.e. the condensation reaction between a carbonyl and an amine. However, the judicious choice of these two building blocks is critical given that many COF forming reactions can lead to an inherent disorder if such a pathway is available. Examples of disorder in 2D-COFs due to both inherent growth mechanisms and reaction pathways will be given and their influence on ion sieving membranes will be discussed. A 2D-COF with negatively charged carboxylated pores, where disorder is minimized, has been shown to be highly charge and size selective for ion conductivity for a series of tetraalkyl ammonium cations. Progress on membranes for desalinization and small ion separations such as Li ion separation from brines using negatively charged, positively charged and zwitterion pores will also be presented.