We developed a habitat augmentation strategy for the Quinebaug River (Connecticut and Massachusetts, USA) in order to reduce impacts on fish habitat, water temperature and pollutant concentrations attributable to consistently low water flows. Using the MesoHABSIM approach and a uniform continuous under‐threshold (UCUT) analysis of simulated habitat time series, we determined allowable periods of low‐flow conditions that follow natural patterns. The amount of water necessary to achieve the required habitat levels was calculated for various river restoration scenarios. We also created a set of detailed rules for a habitat augmentation release that applies short ‘pulses’ of water to increase habitat availability and mitigate the effects of persistent drought conditions. A set of flow chart templates was developed to guide the planning of an augmentation scheme by utilizing flow releases from reservoirs. To test our augmentation procedures, we performed evaluation tests by applying the rules to flows that occurred in 1994 (a drought year). The test showed that the number of flow interventions necessary was limited, underlining the feasibility of a pulse‐based approach. Copyright © 2008 John Wiley & Sons, Ltd.