An eco‐hydraulic model is described, namely, “WW‐Eco‐tools.” The model is composed of hydro‐morpho‐dynamic, habitat, and population models. Fish habitat suitability models assess habitat quality, based on abiotic parameters, namely, flow velocity, depth, and substratum data. These are all derived from a hydro‐morpho‐dynamic model. The relationships between parameters and habitat features are represented as suitability index curves (SI curves) or fuzzy rules. To dynamically simulate fish species, two different population models are developed. The first is converted from a logistic population concept. Its model parameters are related to time‐dependent fish habitat conditions, namely, weighted usable areas and an overall suitability index. The second model is based on a matrix population concept, with numbers as the only state vector. Age‐specific fecundities and survival rates depend on the habitat qualities defined in the matrix population model. The eco‐hydraulic model provides very promising results, highlighting the fundamental role of temporal variability of hydro‐morphological parameters in structuring habitat and populations of fish species. Using this software to anticipate water management changes, simulated population trends can help decision‐makers optimize management measures.