Since inter-annual climatic variability influences composition and structure of seed bank and extant vegetation, it is expected that it also affects the relationship between both compartments at small scales along time. We hypothesize that seed bank and aboveground vegetation are closely and sequentially linked at small spatial and time scales. We conducted a field spatially explicit investigation to explore the spatial and temporal relationship between both compartments. Abundance, composition and spatial structure at different small-scales of seed bank and aboveground vegetation were analysed through 100 permanent plots during two consecutive (dry and wet) periods of growth. Following a conceptual transition path model, we analysed changes in correlation values in composition and spatial aggregation between both compartments along time including seasonal variations of seed bank. Shape of spatial structures were evaluated using partial Mantel correlograms. Annuals and perennials guilds were studied separately. During the wet year, annuals increased their aerial spatial aggregation and cover, whereas the opposite happened for perennials. Density and spatial aggregation of the seed bank increased for both guilds in the two seasons following the rain period, especially in annuals. The clumped structure of the transient seed bank is a consequence of the addition of spatial structure of extant vegetation and the persistent seed bank. Expression of the persistent seed bank is much lower during the dry period for the annual guild. In spite of the strong yearly variability, the community maintained a highly structured spatiotemporal pattern. The mechanisms promoting this stability differed for annual and perennial guilds. Temporal persistence in perennials relied mainly in established plants longevity, whereas annual guild persistence depended solely on seed bank. This tight structure was coherent with the existence of successional dynamics in the community, although persistent seed bank could moderate the pace. Longer term studies of seed bank–standing vegetation dynamics are required to fully understand this process.