A river in drought looks merely lower for a long time before anything dramatic happens. The ecological damage begins much earlier, in temperature and chemistry rather than in visible water level.
Less water heats faster
A shallower channel has less volume to absorb the same solar input, so water temperature rises faster during the day and swings more widely between afternoon and dawn.
Cold-water fish such as trout and salmon have narrow thermal tolerances. As temperature climbs their metabolic demand increases at exactly the moment food and oxygen become scarcer.
The result is a squeeze rather than a single lethal event. Fish stop feeding, stop growing and become vulnerable to disease well before any water reaches a fatal temperature.
Oxygen falls as demand rises
Warmer water holds less dissolved oxygen, and slower flow reduces the turbulence that mixes air into it. Both effects move in the same direction at once.
Meanwhile decomposition of organic material continues and often accelerates in warmer water, consuming oxygen from a supply that is already shrinking.
Nighttime is the worst period, since aquatic plants and algae respire without photosynthesizing and oxygen reaches its daily minimum in the hours before sunrise.
Concentration changes the chemistry
Whatever enters a river from farmland, streets and treatment plants is diluted by flow. When flow drops, the same load arrives into far less water.
Nutrient concentration rises, which can trigger algal growth that further depresses oxygen when the bloom dies and decomposes.
Salts and metals concentrate the same way, and species with limited tolerance encounter conditions they would never meet at normal discharge from identical inputs.
Connectivity breaks before the channel does
As riffles between pools go dry, a continuous river becomes a chain of isolated pools. Fish that were free-ranging are trapped in whatever pool they occupied.
Each pool then functions as a closed system with finite oxygen, accumulating waste and concentrated predators, and conditions inside deteriorate on a schedule of days.
Migratory species suffer separately, since a barrier that appears mid-season can block access to spawning or rearing habitat for an entire year class.
Recovery depends on refuges
Populations rebuild from individuals that survived in deep pools, spring-fed reaches and cool tributaries, so those places determine how quickly a river repopulates.
Management that protects groundwater inputs and shade over small headwater streams is therefore protecting the seed stock for everything downstream.
Where refuges have been lost to channel straightening, water withdrawal or removal of streamside trees, a river can be reconnected by rain and still stay empty for years.