The ridge-and-valley roughness structure of a polyamide reverse osmosis (RO) membrane has a paramount impact on its separation performance. We show that this surface roughness appearance was shaped by gas nanobubbles confined between the polyamide rejection layer and the substrate. Performing interfacial polymerization (IP) under alternative confinement conditions led to drastically different surface morphologies, e.g., smooth polyamide surface formed at support-free aqueous/organic interfaces whereas crater-like features formed in inversed IP. For the first time, we demonstrated the collapse of fully hydrated balloon-like nodules into dehydrated leaf-like and donut-like roughness features during membrane drying by performing an in-situ atomic force microscopic characterization. Deformation of roughness features caused by dehydration was not fully reversible, which correlates well with the dramatic reduction of membrane permeability upon drying. Our study provides a fundamental framework for the surface roughness formation in RO membranes, which is critical for advancing roughness control technologies with enhanced membrane performance.