We present a new hydro-morphological index of diversity (HMID), a tool aimed for use in river engineering projects and firstly developed at gravel-bed streams in Switzerland, but intended for a broader use. We carried out field work with extensive hydraulic and geomorphic data collection, conducted correlation analysis with hydro-morphological variables, formulated the HMID, and analyzed the correlation between HMID and a visual habitat assessment method. The HMID is calculated by means of the coefficient of variation of the hydraulic variables flow velocity and water depth, which have been demonstrated to sufficiently represent the hydro-morphological heterogeneity of alpine gravel-bed stream reaches. Based on numerical modeling, the HMID can be calculated easily for a comparison of different alternatives in river engineering projects and thus achieves predictive power for design decisions. HMID can be applied at a reach-related scale in engineering programs involving geomorphic measures that aim at the enhancement of habitat heterogeneity of a stream. However, the application of HMID has to be integrated with evaluations of the long-term streambed evolvements that are considered at a catchment scale and strongly related to the sediment regime of the stream under study.