Downstream migration of immature salmonids (smolts) may be associated with severe mortalities in anthropogenically altered channels. In Pacific salmon, several investigations have suggested the use of the dominating surface orientation of smolts to improve fish by-pass structures in large and deep hydroelectric reservoirs. The present study tested the use of a surface orientated travelling screen to guide Atlantic salmon (Salmo salar L.) and brown trout (Salmo trutta L.) smolts past a water abstraction site in a shallow lowland stream. The percentage of total discharge abstracted from the stream was included in the analyses. Indigenous migrating smolts were trapped, PIT tagged and subsequently released upstream of the water abstraction site. Releases shifted between a present or absent travelling screen. The migration success of the released smolts was evaluated using a trap situated downstream of the water abstraction site. There was no evidence that the surface oriented travelling screen had any influence on the probability of fish passing the water abstraction site. However, for both species, the probability of successful migration past the water abstraction site correlated negatively with the abstracted percentage of the total daily stream discharge. These findings may have important management implications because they suggest that short term changes in the percentage of total stream discharge abstracted may have consequences for the downstream migration success of smolts. Copyright (C) 2009 John Wiley & Sons, Ltd.