Atlantic salmon (Salmo salar) of southern European origin migrating to the Norwegian Sea currently encounter anomalously high sea-surface temperatures, and returning adults are of low mean condition factor. For the River North Esk (Scotland), time-series changes in river age-structure of emigrant smolts and returning one- and two-sea-winter (1SW and 2SW) adults are assessed. A comparison of the river age-structure of returning adults (1977–1999) with that of their respective annual emigrant smolt cohorts shows no evidence of river age-related bias in survivorship at sea. Evidence is presented of a possible transgenerational, or maternal, influence (poor somatic condition of spawners) driving reduced quality of emigrant S2 smolts in the North Esk. This effect is concurrent with an influence of freshwater climate as indicated by the North Atlantic Oscillation Index (NAOI). The maternal influence and NAOI variation in the winter immediately prior to smolt migration jointly explain approximately 29 (S2) and 17% (S3), respectively, of the variation in the mean size of smolts over the period 1975–2010. Run-timing of 1SW adult cohorts returning to Scotland shows recent delays. Variation in river flow did influence mean return date for the River Tweed, but adult condition factor, which itself shows temporal trends likely to be associated with ocean climate change, was the primary significant explanatory variable for run-timing in the rivers North Esk and Tweed. Overall, in years of poorer adult condition, 1SW salmon stay at sea longer.