Although fire does not directly affect aquatic habitats, the ramifications of fire can have strong effects on these habitats. Most of these lower the productivity of these habitats in the short term. One of the immediate effects can be a warming of a small stream due to fire. This may kill some animals, however, due to the high specific heat of water the effect is minor. If the fire is severe, it may burn away riparian vegetation, causing more sun to be able to hit and warm the water, having detrimental effects on fish. However, fallen trees in a watercourse actually improve fish habitat.

One of the most potent effects of fire on aquatic ecosystems is the amount of erosion it causes. After a fire, the first large storm of the year will dump masses of ash and mud into a watercourse. This can kill most or all of the acquatic organisms in the area. Along with the sediments, large amounts of nitrogen and other nutrients may be washed into the creeks of an area.

Fire often increases the severity of floods and droughts in a watershed as well. Because most of the water falling during a rain event immediately washes into nearby creeks, flooding in a fire-impacted ecosystem can be extremely severe. These floods carry sediment which can be harmful to aquatic organisms. Conversely, since rainfall does not get a chance to soak in, the groundwater level often drops after a fire and watercourses may become lower or dry up completely. Although this may be partially offset by the lack of plants using water in the watershed, it is still a strong influence. Obviously, an aquatic watershed will not be healthy if a normally flowing creek is dry.

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