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Environmental conditions vary spatially and temporally, providing organisms with both challenges and opportunities. Animals have evolved a spectacular variety of migratory behaviours to take advantage of environmental variation, particularly in cases where this variation is predictable. The spatiotemporal pattern of migratory movements displayed by a population or species can be thought of as the evolutionary outcome of trade-offs amongst life history traits. As such, the study of animal movement in relation to environmental heterogeneity can yield valuable insights into the proximate and ultimate drivers of migratory behaviours as well as the behavioural mechanisms underpinning genetic structure. Against this background, the overarching aim of this thesis is to investigate the role of environmental heterogeneity in shaping locally-adapted migratory behaviours, finescale genetic structure and physiological performance in populations of wild brown trout (Salmo trutta) and Atlantic salmon (Salmo salar). Using telemetry data from passive integrated transponder (PIT) tags, I investigated the fine scale spatiotemporal patterns of spawning-related movements of brown trout between a feeding lake and two spawning streams (one inflowing, one outflowing, separated by < 100 m) over two spawning seasons. The timing of seasonal, daily and diel movements was strongly associated with variation in photoperiod, stream height and moon phase. Movement activity was highest at night, and particularly on nights with minimal lunar illumination and high water levels, suggesting that trout synchronise their spawning movements with environmental conditions that minimise their visibility to predators. Males began their movements between the lake and vii streams significantly earlier in the spawning season than females (protandry) and were generally more active. A substantial proportion of trout entered both spawning streams during the spawning periods, providing potential sources of gene flow between the two streams. However, Bayesian analyses revealed the existence of subtle genetic differentiation between juvenile trout sampled in the two streams and indicated that gene flow was strongly asymmetrical in a predominantly downstream (i.e. inflow to outflow) direction. Thus, natal dispersal between the two streams appears to be more common amongst trout that hatch in the inflow than the outflow. These findings have important implications for genetic diversity and local adaptation of fish stocks in fluvial and lacustrine environments. The collection of PIT-derived data in fluvial habitats is often hindered by the fragility of PIT antennae when exposed to high flows and flotsam. In Chapter 3 I present a novel PIT antenna design I developed for use in flood-prone spatey rivers. This design allows flotsam to pass without causing significant damage to antennae and was crucial for collecting the data used in Chapters 4 and 5 and in Appendix A. The performance of migratory populations can be strongly influenced by factors that affect the physiology or survival of migrants in any encountered habitat. I therefore investigated whether the acanthocephalan endoparasite Pomphorhynchus laevis causes a habitat-specific (i.e. freshwater or saltwater) pathology in Atlantic salmon smolts. Peculiarly for the species, the Irish strain of P. laevis uses salmonids, instead of cyprinids, as its preferred definitive hosts. Despite observing high prevalence of the parasite amongst wild smolts and high infection intensities in some individuals, I found no evidence of a pathological effect of infection in fresh or salt water. viii However, I did demonstrate that this freshwater parasite can survive in smolts in salinities similar to those found in coastal waters for at least 72 hours. Thus, the coastal roaming behaviour of Irish sea trout may have facilitated the colonisation of Irish river systems, resulting in the exceptionally widespread distribution of the parasite in Ireland. Collectively, these results contribute to our knowledge of how environmental heterogeneity influences the movement, performance, distribution and genetic structure of organisms in aquatic environments. As modern environmental changes occur at an unprecedented pace, such knowledge may provide us with the ability to anticipate, and perhaps even ameliorate, the impacts that anthropogenic activities have on migratory species.