The bundling of densely packed free-standing nanorods/nanotubes in a liquid environment, or the 'nanocarpet effect', has a direct impact on the stability of nanostructures used for chemical and biological sensors. Using glancing angle deposition, we prepared four different structures: vertically aligned, tilted, zigzag, and square spring Si nanorod arrays, and compared their stabilities after water treatment. We found that although the tilted nanorods were bent in the nanorod tilting direction, they did not form nanorod bundles, and this structure was the most stable one. The larger the tilting angle, i.e., the more inclined the nanorod was to the surface, the more stable the structure. We also found that the quasi-vertical nanorod structures, the zigzag and square spring structures, showed improved stabilities compared to vertically aligned nanorods. Furthermore, by properly depositing a capping layer on top of the vertically aligned nanorods, the structure became mechanically very stable while the high porosity nature of the nanorod array was maintained. This work is helpful for designing stable nanostructures used in a liquid environment.