In the northern coast of Spain there are rivers with Atlantic salmon populations. In the upper reaches of one of these streams, river Pas, the effectiveness of habitat enhancement measures was evaluated, under different instream flow conditions. By means of the Instream Flow Incremental Methodology and using a two dimensional hydraulic model (River2D, Steffler P (2000) Software River2D. Two Dimensional Depth Averaged Finite Element Hydrodynamic Model. University of Alberta, Canada), the potential value of stream habitat for different salmon development stages requirements was measured by Weighted Useable Area (WUA). This habitat evaluation was carried out for the unmodified stream reach, which represent the control or natural conditions. Habitat improvement measures (alternate deflectors and low dams) were simulated in the original riverbed topography. Over this modified base, habitat was estimated running River2D again. By comparing the salmon habitat evaluations in the control conditions with those obtained under those improvement conditions we have been able to assess the effectiveness of each one, and the instream flow environment at which maximum improvement is reached. The maximum habitat improvement was obtained around 10 m 3 /s for the adult salmon, and for the fry and parr it was around 6 m 3 /s. However, the habitat simulation results show that with both improvement measures, under a natural flow regime the mean annual habitat increases around 1% of the WUA in relation to the control conditions, which is not a significant improvement. A similar small WUA increase was obtained when changing the bed topography, considering geomorphological adjustments due to the new erosion and sedimentation areas caused by the presence of these structures. Therefore, these types of habitat improvement measures are not recommended in these stream reaches.