When hydrophobic surfaces are in contact with water in ambient conditions a layer of reduced density is present at the interface, preventing the intimate contact between the two phases. Reducing the extent of this layer by degassing the water can have remarkable implications for the interaction between the two phases. The enhanced proximity between a hydrophobic polymer film and an aqueous solution can induce a self-assembled nanostructure on the solid surface through the development of an electro-hydrodynamic instability, due to the adsorption of the water-ions (hydronium and hydroxyl) at the interface. The self-assembled structure spontaneously relaxes back to the original flat morphology after few weeks at room temperature. This instability and the self-assembled structure are controlled by the hydrophobic surface charge, which is determined by the pH of the aqueous phase, and by the amount of gas dissolved. This effect can be easily adjusted to modify different hydrophobic polymeric substrates at the submicrometer level, opening pathways for producing controlled patterns at the nanoscale in a single simple waterborne step.