A routine to predict the performance of cross-flow hydrokinetic turbines, based on the Blade Element Momentum theory, for site assessment purposes is here presented. The routine uses as input the flow data obtained with the open-source marine circulation code SHYFEM. The routine consists in a Double Multiple Stream Tube model making use of 1D flow simplifications for fast analyses. The dynamic stall sub-model and two original sub-models, implemented to include the effects of blade tip losses and the lateral deviation of streamlines approaching the turbine, have been validated versus results of 3D and 2D CFD simulations. As a case study, the tool is applied to an area of the northern Adriatic Sea in order to quickly identify locations with the highest hydrokinetic potential and, at the same time, to find the most efficient turbine aspect ratio and configuration (single or paired turbines) taking into account the bathymetric constraints. The results show that turbines, with short aspect ratio, and paired turbines (with the same overall frontal area of a single rotor) can give the best power outputs thanks to higher flow speeds available at the top of the water column and more favorable Reynolds number and distribution of tip speed ratios along the blade.