Intact ecological connectivity involves open exchange pathways for matter, energy and organisms along longitudinal, vertical, lateral and temporal axes. For salmonids, intact longitudinal conductivity ensures that fish can migrate between habitats, and intact vertical connectivity fosters development of favourable intragravel environments for incubating embryos. Here, we present an overview of our studies of vertical and longitudinal connectivity as they relate to the different life stages of anadromous brown trout in regulated rivers. Our studies of vertical connectivity have shown that changes in surface discharge were more tightly coupled to changes in the intra-gravel environment or hyporheic zone in an unregulated river than in two regulated rivers. In terms of oxygen conditions for incubating brown trout eggs, conditions were more favourable in the unregulated river than in the regulated rivers, with the poorest conditions in the river being lack of minimum flow requirements. Our studies of longitudinal connectivity have examined both upstream and downstream migration of anadromous trout through two nature-like passageways at Finsjö in the River Emån, southern Sweden. On the basis of telemetry and PIT-tag studies, we found that passage efficiency was high, ranging from 89 to 100%. Attraction efficiencies for the passageways were more variable, ranging from 50 to 89%, depending on passageway and year. Densities of brown trout upstream of the passageways were higher in two of the four years after the passageways were built than during pre-passageway years or in other sections of the river. An average of 51% of the downstream-migrating smolts and 57% of the kelts swam past both dams at Finsjö, and 15% of the smolts reached the Baltic Sea. Further remedial measures, particularly for downstream migrants, are needed to attain a fully intact longitudinal connectivity that operates for both upstream and downstream migrants.