Large blooms of cyanobacteria, primarily Aphanizomenon flos-aquae, are linked to poor water quality in Upper Klamath Lake,
Oregon. High pH and high un-ionized ammonia concentrations are associated with the blooms when algae are actively growing,
followed by low dissolved oxygen (DO) conditions when the blooms decline in mid- to late summer. Over a 12-year study period,
algal biomass was strongly related to total phosphorus concentration (TP) and pH. Minimum water column DO was strongly related
to net negative changes (i.e., declines) in algal biomass during July and August. The severity of both low DO and high ammonia
was positively related to water column stability, which was dependent on wind speed. Bloom dynamics, coupled with climate,
dominated year-to-year variability in water quality dynamics in Upper Klamath Lake. These data provide the empirical basis for
previous research linking high mortalities of endangered sucker species with years of low wind and high water column stability.