Habitat structure and complexity influence the structuring and functioning of fish communities.Habitat changes are one of the main pressures affecting estuarine systems worldwide, yet the degree and rate of change and its impact on fish communities is still poorly understood. In order to quantify historical modifications in habitat structure, an ecohydrological classification system using physiotopes, i.e. units with homogenous abiotic characteristics, was developed for the lower Lima estuary (NW Portugal). Field data, aerial imagery, historical maps and interpolation methods were used to map input variables, including bathymetry, substratum (hard/soft), sediment composition, hydrodynamics (current velocity) and vegetation coverage. Physiotopes were then mapped for the years of 1933 and 2013 and the areas lost and gained over the 80 years were quantified. The implications of changes for the benthic and demersal fish communities using the lower estuary were estimated using the attractiveness to those communities of each physiotope, while considering the main estuarine habitat functions for fish, namely spawning, nursery, feeding and refuge areas and migratory routes. The lower estuary was highly affected due to urbanisation and development and, following a port/harbour expansion, its boundary moved seaward causing an increase in total area. Modifications led to the loss of most of its sandy and saltmarsh intertidal physiotopes, which were replaced by deeper subtidal physiotopes. The most attractive physiotopes for fish (defined as the way in