Hydrological connections between river channels and their adjacent floodplains facilitate the flux of organisms and nutrients and access to increased habitat and new resources. Hydrological connections also deliver water subsidy and potentially disturb (through hydraulic forces) floodplain ecosystems. This study investigates the role of hydrological connectivity as a driver of patterns in wetland plant assemblages in billabongs on the floodplain of an Australian dryland river, exploring indirectly the relative importance of the mechanisms of flux, subsidy and disturbance. Wetland plants were surveyed in billabongs across gradients of hydrological connectivity and depth. Surveys were accompanied by experiments examining germination from the soil seed banks of each site under submerged and waterlogged conditions. The patterns in extant and germinant plant communities in relation to connectivity and depth gradients were used to infer the relative importance of the connectivity-related mechanisms of flux, subsidy and hydraulic disturbance in structuring wetland plant communities. Depth influenced both extant and germinating plant communities. Shallow billabongs supported a greater diversity and abundance of plants, and greater numbers and diversity of germinable seeds in the seed bank. Germination of seeds was greater in waterlogged soils than submerged soils. Thus, the main controls of plant abundance in wetlands appear to be availability of waterlogged soil habitat for germination and absence of light limitation for growth. Hydrological connectivity did not influence the abundance of plants or germinable seeds, but did influence species presence-absence in growing vegetation; this effect did not extend to the germinating community. Thus, hydrological connection does not appear to influence wetland vegetation by facilitating the movement of propagules between habitats. Instead, the patterns observed are consistent with hydrological connection providing a cue for germination through the delivery of water, and by modifying hydraulic habitat.