Organisms inhabiting estuaries are increasingly exposed to both natural and anthropogenic disturbances, such as tidal fluctuations, pollution, and rising temperatures. Genetic diversity is essential for species to adapt to these environmental challenges, as reduced diversity can lead to inbreeding depression and reduced adaptive potential. Here, we genotyped the golden kelp Ecklonia radiata, a key habitat-former in temperate Australia, across eight sites within Sydney Harbour, an urban estuary located in Australia's largest city. Using 2107 neutral single-nucleotide polymorphisms (SNPs), we characterised the genetic diversity of the golden kelp, described its spatial genetic structure and tested for signatures of divergent selection across the harbour. Our analysis revealed the presence of two genetic clusters (F_ST = 0.129) with small effective population sizes (N_{e (inner)} = 183.2; N_{e (outer)} = 16.7). The relatively low heterozygosity and elevated inbreeding coefficients found in both populations suggest high rates of self-fertilisation across the harbour. The strong population structure was consistent with significant differences in E. radiata morphology across the harbour. Genotype-environment analyses revealed strong associations with light, organic matter, copper, manganese and temperature, suggesting adaptation to local environments. These findings emphasise the importance of considering local adaptation and population structure in restoration strategies not only in Sydney Harbour, but also other estuaries facing similar challenges.