We examined the survival and progression rates of 101 anadromous brown trout Salmo trutta L. post-smolts from two Danish river systems, Karup and Simested, with acoustic telemetry as they migrated through a large Danish fjord system (the Limfjord). No fish were documented to residualize permanently within the fjord, and the minimum survival in the fjord was low (26%) while the mortality per km of migrated linear distance (0.8% km−1) was similar to that found in adjacent and smaller Danish fjords. Survival was positively correlated with length (P = 0.003) but not with condition and river of origin. The fjord has an eastern outlet into the Kattegat and a western outlet into the North Sea, but the western outlet did not exist until 1825. No fish left the fjord in the western direction in the study and all surviving fish (n = 20) left the fjord in the eastern direction. The results suggest that fish from rivers Karup and Simested may have over time become adapted for leaving the Limfjord in the eastern direction and that predation rates and environmental characteristics of the fjord are more important for the fjord's ability to function as a suitable growth habitat for post-smolts than size and the availability of food within it.