Seed mortality due to low winter temperatures has been proposed as an explanation for the lack of seedling recruitment in natural populations of the rare riparian species Alnus maritima, but other factors such as the absence of essential root symbionts or canopy clearing disturbances could also limit establishment of new individuals. We investigated whether any of these factors could be identified as preventing recruitment into existing seaside alder populations. Stratification studies showed that not only can seeds withstand low temperatures, longer periods of cold stratification promote earlier seed germination and expand the temperature range for germination. Root microbiome studies unexpectedly found that seedlings inoculated with the native microbiome prior to planting had lower survival compared to uninoculated individuals, and uninoculated individuals declined in survivorship after natural inoculation in the field. Canopy disturbance by burning or clipping vegetation promoted neither seedling growth nor survival initially, with seedling survival lower in burned plots due to the release of an aggressively growing competitor. Our results show that physiological stress by microbial symbionts and competition with other species are likely primary limiting factors—more so than seed mortality from low temperatures—and should be the focus of future conservation efforts.