Abundance–Biomass Comparison (ABC) models, first described for marine benthic macrofauna, have been applied successfully to other marine and terrestrial/freshwater fauna but never to ecotonal communities. In particular, to our knowledge, ABC models have not been applied to hyporheic communities. This study represents the first application of ABC models to hyporheic assemblages. We aimed at testing the effectiveness of ABC models in describing the perturbation of hyporheic communities subjected to an existing/known disturbance. To this end, we applied the models to the hyporheic community of an Apennine creek, where the hyporheic waters of the upstream stretch were uncontaminated, whereas those of the downstream stretch were contaminated by ammonium. We also tested separated models for the summer and winter periods to account for potential variability due to season. ABC models provided a satisfactory description of the hyporheic community changes due to ammonium by showing the abundance dominance curve overlying that of the biomass in the downstream stretch contrarily to what was observed in the upstream stretch. However, ABC models did not highlight any significant seasonal effects. Our results showed that ABC models have the potential to be used as assessment tools for ecological quality of hyporheic zones in temperate regions.