The population dynamics of rock fern Asplenium septentrionale in Estonia was monitored from 1994 to 2020; the data were analysed to understand how the rhythm of local weather variables affects the population condition and renewal. Both fern clump size and life stage (sporeling, premature, mature, senescent) structure of the population were studied. Our results indicate that the population has been stable, with a high proportion of reproductive adults. Precipitation distribution through all seasons of the year had a major impact on population recruitment. June was the key period of the year determining the survival of young sporelings. Higher rainfall in the previous year supported higher numbers of premature clumps in the following year. The number of mature fern clumps was most influenced by weather conditions during winter months and precipitation at the end of summer. The long-term survival of mature clumps might be threatened if periods without rainfall extend into the growing season and occur during consecutive years. Monitoring methods of nationally protected fern species should be improved by including individual-based observations on life stage transitions of young sporophytes (sporeling to premature, premature to mature) for predicting future trends in population conditions.