Lakes are complex ecosystems composed of distinct habitats coupled by biological, physical and chemical processes. While the ecological and evolutionary characteristics of aquatic organisms reflect habitat coupling in lakes, aquatic ecology has largely studied pelagic, benthic and riparian habitats in isolation from each other. Here, we summarize several ecological and evolutionary patterns that highlight the importance of habitat coupling and discuss their implications for understanding ecosystem processes in lakes. We pay special attention to fishes because they play particularly important roles as habitat couplers as a result of their high mobility and flexible foraging tactics that lead to inter‐habitat omnivory. Habitat coupling has important consequences for nutrient cycling, predator‐prey interactions, and food web structure and stability. For example, nutrient excretion by benthivorous consumers can account for a substantial fraction of inputs to pelagic nutrient cycles. Benthic resources also subsidize carnivore populations that have important predatory effects on plankton communities. These benthic subsidies stabilize population dynamics of pelagic carnivores and intensify the strength of their interactions with planktonic food webs. Furthermore, anthropogenic disturbances such as eutrophication, habitat modification, and exotic species introductions may severely alter habitat connections and, therefore, the fundamental flows of nutrients and energy in lake ecosystems.

The total world catch from marine and freshwater wild stocks has peaked and may be slightly declining. There appear to be few significant resources to be developed, and the majority of the world's fish stocks are intensively exploited. Many marine ecosystems have been profoundly changed by fishing and other human activities. Although most of the world's major fisheries continue to produce substantial sustainable yield, a number have been severely overfished, and many more stocks appear to be heading toward depletion. The world's fisheries continue to be heavily subsidized, which encourages overfishing and provides society with a small fraction of the potential economic benefits. In most of the world's fisheries there is a “race for fish” in which boats compete to catch the fish before a quota is achieved or the fish are caught by someone else. The race for fish leads to economic inefficiency, poor quality product, and pressure to extract every fish for short-term gain. A number of countries have instituted alternative management practices that eliminate the race for fish and encourage economic efficiency, use lower exploitation rates that deliberately do not attempt to maximize biological yield, and encourage reduced fishing costs and increased value of products. In fisheries where this transition has taken place, we see the potential for future sustainability, but in those fisheries where the race for fish continues, we anticipate further declines in abundance, further loss of jobs and fishing communities, and potential structural change to marine ecosystems.

One of the most spectacular phenomena in nature is the annual return of millions of salmon to spawn in their natal streams and lakes along the Pacific coast of North America. The salmon die after spawning, and the nutrients and energy in their bodies, derived almost entirely from marine sources, are deposited in the freshwater ecosystems. This represents a vital input to the ecosystems used as spawning grounds. Salmon-derived nutrients make up a substantial fraction of the plants and animals in aquatic and terrestrial habitats associated with healthy salmon populations. The decline of salmon numbers throughout much of their southern range in North America has prompted concern that the elimination of this "conveyor belt" of nutrients and energy may fundamentally change the productivity of these coastal freshwater and terrestrial ecosystems, and consequently their ability to support wildlife, including salmon. If progress is to be made towards understanding and conserving the connection between migratory salmon and coastal ecosystems, scientists and decisionmakers must explore and understand the vast temporal and spatial scales that characterize this relationship.

Detecting and forecasting the effects of changing climate on natural and exploited populations represent a major challenge to ecologists and resource managers. These efforts are complicated by underlying density‐dependent processes and the differential responses of predators and their prey to changing climate. We explored the effects of density‐dependence and changing climate on growth of juvenile sockeye salmon and the densities of their zooplankton prey in the Wood River system of southwestern Alaska. We fit dynamic time‐series models to data collected between 1962 and 2002 describing growth of juvenile sockeye, timing of spring ice breakup, and summer zooplankton densities. The timing of spring breakup has moved about seven days earlier now than it was in the early 1960s. Our analyses suggest that most of this shift has been a response to the warm phase of the Pacific Decadal Oscillation that persisted from the mid‐1970s to the late 1990s. This progression toward earlier spring breakup dates was associated with warmer summer water temperatures and increased zooplankton (especially Daphnia) densities, which translated into increased sockeye growth during their first year of life. The number of spawning adults that produced each year class of sockeye had a strong negative effect on juvenile sockeye growth rates, so that the size of the density‐dependent effect was, on average, twice as large as the effect of spring breakup date. These results highlight the complexity of ecological responses to changing climate and suggest that climate warming may enhance growing conditions for juvenile salmonids in large lakes of Alaska.