The links between hydrology, hydrochemistry and salmonid ecology were examined in an interdisciplinary study of the effects of hyporheic water quality on the survival and the development of salmonid ova. Three catchments located in the northeast of Scotland were examined. Work focussed on the Newmills Burn, a degraded agricultural catchment. Complementary studies were also undertaken on the Pow Burn, a comparative agricultural catchment, and the Girnock Burn, a contrasting semi-pristine upland catchment. The relative importance of sediment transport, groundwater-surface water (GW-SW) interactions and hydrochemistry, for the survival and development of salmonid ova, was assessed between spawning in autumn, and hatch in spring. Hydrochemical, hydrometric, isotopic and modelling techniques were applied to the problem in an evolving, serial approach to investigation. The infiltration of fine sediment to the streambed was not sufficient to explain observed fine scale spatial variability (<1m), nor complex spatial patterns of sub-surface hydrochemical change. Hydrochemical and piezometric data indicated that the observed spatial and temporal patterns could be explained by variable contributions of chemically reduced groundwater to the hyporheic zone. At the catchment scale, gross differences in land-use and channel characteristics substantially affected GW-SW interactions and consequently in-redd water quality. At the reach scale, local GW-SW interactions were controlled by geomorphology and riparian sedimentary stratigraphy. At the scale of individual redds, the influence of groundwater generally increased with depth into the hyporheic zone. Dissolved oxygen (DO) levels were implicated as the dominant control on in-redd mortality. Embryo survival and development correlated with mean DO concentrations. Mortality rates from samplers located within artificial redds ranged from 0-100% and showed a significant inverse relationship with mean DO concentrations (r2 = 0.85, P < 0.01). Where embryos survived, low DO affected rates of development. Embryos exposed to low DO concentrations retained a higher portion of the yolk sac mass near to hatch than those developing in more favourable conditions.