The research focusses on the river Lugg – a cross-border catchment and major tributary of the river Wye, the most important Atlantic salmon river in England and Wales. The problem of declining Atlantic salmon populations in the catchment is addressed through investigating recruitment from egg fertilization to the emergent life stage and beyond using multiple field-based and laboratory techniques. The approach adopted is multidisciplinary and addresses the need for holistic approaches to habitat degradation which is increasingly recognised as systemic in nature; often with multiple stressors acting interactively. The initial premise of deleterious fine sediment infiltration into spawning gravels was addressed by a sediment fingerprinting study to ascertain the provenance of infiltrated redd sediment from a range of land-use types. In addition, nine artificial redd sites were constructed and assessed for fine sediment infiltration, intragravel dissolved oxygen levels, intragravel flow velocity and other hyporheic pore water characteristics, in relation to survival to emergence over two field seasons. A study examining the quality of emergent fry was also carried out using fitness tests and individual stress levels. Additionally, a study on long-residence groundwater infiltration into the incubation environment was carried out. The main fine sediment contributor was derived from agricultural sources, particularly during wetter periods. The average contribution of fine sediment from agricultural sources was 60%. Survival ranged from 12% to 70% during the 2008 flood season and from 76% - 93% during the 2009 dry season. Fine sediment mass as a stand-alone index was only weakly correlated with survival but is thought to influence other factors; medium strength correlations of survival with dissolved oxygen, intragravel flow velocity and oxygen supply in particular were observed. Evidence of groundwater-surface water interactions were detected at two of three sites investigated and is proposed as an additional controlling mechanism for embryonic survival in the catchment. Sublethal fitness tests demonstrated variations between cohorts in the 2009 period despite a relatively small range of oxygen concentrations. The results highlight both temporal and spatial variations in spawning habitat quality, which influence not only survival to hatch but also posthatch fitness.