Spatial genetic structure (SGS) studies contribute to our understanding of gene flow and species dispersal. Only a few studies have linked the spatio-temporal pattern of SGS and intra-specific interactions. Black poplar (Populus nigra L.) is a threatened pioneer riparian tree species along many rivers across Europe. We studied its SGS in cohorts of varying ages at a fine-scale (i.e. at distances including the zone of influence between individuals) to better understand local patterns of dispersal and intra-specific interactions during early life-stages. We genotyped 349 P. nigra individuals in three gravel bars along a 1.6 km reach of the Allier River in the Réserve Naturelle du Val d'Allier, central France. We found high genetic diversity values (He = 0.860) thus identifying this site as important for the conservation of P. nigra genetic diversity. We also found significantly more clones in locations exposed to the river flow compared with less exposed locations. These clones offer mechanical protection and habitat improvement (through facilitation) to individuals in close proximity. A significant fine-scale SGS was observed in the youngest cohort at the gravel bar scale while none was observed in the older cohorts or at the river reach scale. This pattern was confirmed by a reanalysis of published data on the Garonne River. A shift in intra-specific interactions, from facilitation to competition through self-thinning, could explain the loss of SGS in older cohorts. This highlights the importance of shifts in intraspecific interactions through life and their consequence on population genetic structure.