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The effect of hyporheic water quality on developing salmonids was assessed between spawning and hatch. Results from a low‐lying degraded agricultural catchment (Newmills Burn) were compared with those from a near‐pristine upland spawning stream (Girnock Burn), providing a set of comparisons beyond the range of hyporheic conditions present in the Newmills Burn. It was demonstrated that hyporheic water quality in the Newmills Burn varied temporally and spatially as a consequence of variable fluxes of chemically reduced groundwater through heterogeneous drift deposits. Mortality rates from samplers located within artificial redds ranged from 0 to 100% and showed a clear negative relationship with mean dissolved oxygen (DO) concentrations (r² = 0.85, P < 0.01). Where embryo mortality was less than 100%, low DO appeared to affect rates of embryo development. Embryos exposed to lower DO …