Two-dimensional (2-D) numerical simulation and habitat suitability curves for brown trout in the Lima River in northern Portugal were used to predict the velocity suitability index (VSI) for various fish shelter configurations. The modeling results were plotted against fish frequentation rates obtained by Ribi et al. (2014) for juvenile brown trout captured in the Tannenbach River on the Swiss Plateau, and tested in an artificial flume equipped with a lateral embayment. New shelter configurations were analyzed numerically to assess habitat availability for juvenile and adult Lima River trout. Good agreement was achieved between the experimental results and the hydrodynamic simulation results, highlighting similarities between the preferences of brown trout from different regions. The obstacle shape and its placement at the shelter entrance greatly influence the habitat availability. The results of this study include an easy-to-use method to assist water managers in selecting appropriate fish shelter configurations to optimize habitat availability. ; The accepted manuscript in pdf format is listed with the files at the bottom of this page. The presentation of the authors' names and (or) special characters in the title of the manuscript may differ slightly between what is listed on this page and what is listed in the pdf file of the accepted manuscript; that in the pdf file of the accepted manuscript is what was submitted by the author.