While Noung's description of the process of eutrophication is appropriate for estuarine and coastal zones, it is not strictly accurate for freshwater systems, where eutrophication has had its greatest impact.

The limiting nutrient in lakes and rivers is not nitrogen, as it is in the ocean, but is instead phosphorus. As added nutrients leach into the water from the watershed (which may be rural or urban, not strictly agricultural), the added phosphorus drives (algal production through the roof. This increased primary production has a number of devastating consequences on the food web, such as:

  • Change to algal community structure: eutrophication not only increases the absolute concentration of plant matter in the water, but also changes the species composition. As eutrophication progresses, phytoplankton species tend to shift from chlorphytes (green algae) to cyanophytes (blue-gree algae, which are in fact prokaryotic and are sometimes classified as bacteria). This latter group produces a number of highly toxic chemicals which not only kill the aquatic fauna but can also harm humans (Brazil has had a number of mass-mortalities due to cyanobacterial build-up in their reservoirs).
  • Change to the zooplankton and benthic communities: as the algal community structure changes, the primary consumers also undergo a shift from larger bodied individuals (such as Daphnia for zooplankton and mayfly larvae for benthic invertebrates) to smaller bodied individuals. This affects the efficiency of transfer of energy from the primary producers up to the consumers, and ultimately results in a crash in the fish populations. With only smaller bodied prey available, top predator fishes (such as trout, perch, walleye etc.) become extinct, and minnows dominate the system.
  • As noted above, if eutrophication is sufficiently severe, an algal bloom will occur (a solid mat of vegetation that covers the water's surface) and when these algae die, they will sink to the bottom. As decomposition occurs, oxygen become depleted and a fish kill is a likely result. However, it should be noted that this is only problematic for cold-water fishes, as the oxygen depletion will only occur below the thermocline (read about epi-, meta- and hypolimnion for a more detailed discussion of thermal stratification in lakes).
  • Finally, sediments will become loaded with organic nutrients (phosphorus and nitrogen) to the point where even if terrestrial inputs are ceased (as a result of saner farming practises, sewage treatement etc.), nutrient loads in the lakes will not decline for years. In Denmark, for example, despite extensive efforts to reduce nutrient inputs, lake recovery has taken as many as twenty to thirty years in some instances.
As an example of these phenoma, we need only look to Lake Erie. In the 1960s and -70s, Lake Erie became severly eutrophic as a result of industrial and agricultural activity in the western end (near Detroit and Windsor). This resulted in a tripling of nutrient concentrations and algal densities, and a crash in both the benthic invertebrate and zooplankton communities. As a result, the walleye and yellow perch populations suffered massive reductions in density (note that commercial overfishing hasn't helped), and the value of the resource declined significantly. Extensive treatment of effluent was undertaken in the 1970s, and only now is the lake reverting to a state similar to that prior to eutrophication.