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Mycorrhizal restoration benefits are widely acknowledged, yet factors underpinning this success remain unclear. To illuminate when natural regeneration might be sufficient, we investigated the degree mycorrhizal fungi would colonizePopulus fremontii(Fremont cottonwood) 2 years after the restoration of a riparian corridor, in the presence of an adjacent source. We compared colonization levels across plant populations and ecotypes, and from trees in the planted area to those in natural source populations. Four findings contribute to the theory and application of host–symbiont interactions. (1) Median ectomycorrhizal colonization of trees in the planted area was less than one‐tenth of that within natural source populations (p < 0.05), suggesting that even with adjacent intact habitat, sluggish regeneration would make proactive mycorrhizal restoration beneficial. (2) Within the planted area, median ectomycorrhizal and arbuscule colonization of trees sourced from greater distances were less than one‐third of that for trees sourced locally (p < 0.05), suggesting translocation poses barriers to symbioses. (3) Changes in colonization did not align with plant ecotypes, suggesting that geographic scales of selection for plants and fungi differ. (4) Slight increases in median mycorrhizal colonization (from 0% to 5%) were strongly correlated with increased survival for the plant provenance with lowest survival (r² = 46% andr_s = 48%,p < 0.05), suggesting mycorrhizae are particularly beneficial when plants are under stress (including translocation‐induced stress). This study is novel in demonstrating that mycorrhizal regeneration is slow even in the presence of adjacent intact habitat, and that when colonization could seem negligible, it may still have biological significance.