The kinetics for the cleavage of the phosphotriester PDE6D inhibitors 1 (Deltaflexin‐2) and 3 (Deltaflexin‐1) and their derivatives 2, 4 and 5 is presented under various conditions in aqueous solutions. The conversion of the phosphotriesters (1–5) into the phosphodiesters 1**–5** was detected to take place as a major degradation process. In the absence of enzyme, the 4‐acetylthio‐2,2‐dimethyl‐3‐oxobutyl protected compounds (1, 4 and 5) are one order of magnitude more stable than the 4‐acetylthio‐2‐ethoxycarbonyl‐3‐oxo‐2‐methylbutyl protected ones (2 and 3). In cell culture (DMEM) containing fetal bovine serum and l‐glutamine, an intermediary formation of S−S‐dimer competed with the removal of the protecting group after deacetylation of the starting material. In addition, the susceptibility of the compounds to amine nucleophiles as well as their stability under acidic and basic condition were determined in non‐aqueous solutions.