Despite the pressing environmental, economic and social issues surrounding water abstraction, scientific methods for managing its ecological impacts remain in their infancy. In this paper, we demonstrate statistically significant relationships between in-stream ecological condition using macroinvertebrates and the hydrological effect of groundwater abstraction on surface water flows in streams originating from Permo-Triassic sandstone aquifers in the English midlands. Ecological condition was most strongly correlated to the effect of abstraction on medium-low flows (Q75) compared with effects at other flows, water quality, habitat or seasonal effects. Ecological impacts occurred when the effect of abstraction on Q75 flows exceeded 60%. The same relationships were shown among individual macroinvertebrate taxa, validating the biological responses. The hydroecological model has provided a scientific basis for making local decisions on investigation sites and has helped to focus resources to areas at risk of not meeting Good Ecological Status under the Water Framework Directive because of abstraction.