The life of aquatic fauna in streams and rivers depends on hydrological variability with considerable emphasis on minimum discharge in flow regulated reaches. One of the methods used to define ecologically suitable minimum discharges is the physical habitat simulation method (habitat model) which converts the outputs of a hydrodynamic river model into habitat suitability for different aquatic taxa, based on their estimated hydraulic preferences. The application of this method requires the use of dedicated software. One of the current computer programs for habitat simulations in France (EVHA) is not technically up-to-date and had to be replaced. Much more than an update of existing software, HABBY is a new free and open-source program, which will be very useful to estimate ecological flows through aquatic habitat availability and suitability. Compatible with MS-Windows, macOS, and GNU/Linux, HABBY is developed in Python. It does not contain any internal hydrodynamic model but accepts, as inputs, the output files of several commonly used models. It also incorporates three statistical habitat models, including Estimhab, a popular statistical model in France. Moreover, a system of scripts helps to store past studies and facilitates the implementation of complex case studies.