Abstract Depletion‐induced self‐assembly is routinely used to separate plasmonic nanoparticles (NPs) of different shapes, but less often for its ability to create supercrystals (SCs) in suspension. Therefore, these plasmonic assemblies have not yet reached a high level of maturity and their in‐depth characterization by a combination of in situ techniques is still very much needed. In this work, gold triangles (AuNTs) and silver nanorods (AgNRs) are assembled by depletion‐induced self‐assembly. Small Angle X‐ray Scattering (SAXS) and scanning electron microscopy (SEM) analysis shows that the AuNTs and AgNRs form 3D and 2D hexagonal lattices in bulk, respectively. The colloidal crystals are also imaged by in situ Liquid‐Cell Transmission Electron Microscopy. Under confinement, the affinity of the NPs for the liquid cell windows reduces their ability to stack perpendicularly to the membrane and lead to SCs with a lower dimensionality than their bulk counterparts. Moreover, extended beam irradiation leads to disassembly of the lattices, which is well described by a model accounting for the desorption kinetics highlighting the key role of the NP‐membrane interaction in the structural properties of SCs in the liquid‐cell. The results shed light on the reconfigurability of NP superlattices obtained by depletion‐induced self‐assembly, which can rearrange under confinement.