It is becoming extremely challenging to protect the structural and functional integrity of freshwater ecosystems, as many ecological systems face pressures from climate change, population growth and other environmental impacts. However, existing approaches of assessing impacts of external stressors to habitat conditions often neglect the long‐term hydrological changes. This study aimed to develop an integrated modelling framework to assess impacts of different stressors on reach‐scale habitat conditions for benthic macroinvertebrates in a temperate lowland river in central Poland. We coupled hydrological (SWAT+), hydraulic (HEC‐RAS 1D and SRH‐2D) and habitat (CASiMiR) models to predict the response of habitat suitability for the functional group of filter feeders to changes in the catchment for a 135‐m section of the Jeziorka river. Setting up and calibrating individual models required extensive field data collection (e.g., bathymetry field surveys, gauging water levels, discharge and flow velocity measurements and biological sampling). The performance of individual models in simulating discharge, water levels and depth/flow velocity was assessed as satisfactory according to literature. The modelling chain was then applied to compare the effects of three flow scenarios (average, low and high flows). The results showed an overall high value of hydraulic habitat suitability index for filter feeders, with moderately and severely lower values for low and high flow scenario, respectively. The implemented modelling framework performed well could be applied to examine the impacts of climate change and other anthropogenic stressors on reach‐scale habitat conditions. Its practical implementation could be beneficial towards sustainable water resources and environmental flow regime development.