The displacement of single atoms may have detrimental effects on the functionality of nanoparticle photocatalysts. Understanding the atomic-scale phenomena is the key to the rational design of photocatalysts to prevent undesired events during their synthesis and operation. Here, we used high resolution TEM to study such phenomena within seeded rods of CdSe in CdS, mounted with bimetallic particles of Au and Pd. We show the mobility of Pd atoms during deposition and photocatalysis and relate that to photocatalyst degradation processes that limit overall photocatalyst efficiency. We also show the advantage of the bimetallic composition and the specific internal rearrangement of the two metals for better efficiency and stability to provide a more generalized understanding of prospective design principles.