Amphibious plants inhabit environments that undergo seasonal transitions between inundation and desiccation, yet little is known about how these transitions shape their microbiomes. We examined bacterial endophytic communities during such transitions in the amphibious plant Eryngium castrense (Apiaceae) native to California's ephemeral wetlands (vernal pools). Using 16S rRNA sequencing, we examined endophytic communities in roots and shoots across aquatic and terrestrial morphological stages, and compared these endophytic communities with surrounding soil and water microbiomes. Community composition differed most strongly between plant compartments (roots vs. shoots), with additional but weaker differentiation between aquatic and terrestrial stages.  Beta diversity analyses showed plant compartment as the strongest variable in community differentiation, followed by morphological state. Phylogenetically weighted distances explained more variation than abundance-based distances.  In addition, endophytic communities were clearly distinct from soil and water microbiomes within the vernal pool ecosystem. Our results highlight the dynamic nature of microbial communities in response to the seasonal transitions of their amphibious plant hosts, suggesting a complex interplay in ephemeral wetlands that warrants further exploration.