The spatial genetic structure (SGS) of plant populations is determined by the outcome of key ecological processes, including pollen and seed dispersal, the intensity of local resource competition among newly recruited plants, and patterns of mortality among established plants. Changes in the magnitude of SGS over time can provide insights into the operation of these processes. We measured SGS in a population of the clonal aquatic plant, Sagittaria latifolia that had been disturbed by flooding, both before and after the flood. . Over the four-year interval between measurements, we found substantial changes in the magnitude of SGS. In the first measurement (pre-flood), SGS was weak, even over short distances. By contrast, there was substantial SGS in the second measurement (post-flood), particularly over short distances. This change in SGS was accompanied by near complete turnover in the genotypic composition of the population. The genotypic richness of the population (the number of unique clones scaled by the sample size) was halved over the four-year interval. The clonal subrange – the distances between shoots within clones – also shrank considerably, with more than 5% of shoots having clone-mates at distances greater than 10 m before the flood, but fewer than 5% of shoots having clone-mates at distances beyond 2 m afterwards. Clonal turnover and the re-establishment of SGS in clonal populations are both expected following local extirpation and recruitment. These data reveal the genetic signatures of disturbance and a subsequent flush of seedling recruitment and subsequent clonal expansion.