Between July 2009 and October 2011, a new habitat was found for a rarely reported freshwater dinoflagellate species, Thompsodinium intermedium - Comal Springs (Comal County), Texas. In 2011, diel in-situ monitoring in monospecific blooms of this species revealed previously undetected negative impacts on endangered species habitat availability associated with conditions of low flow levels, recorded at the U.S. Geological Survey gage # 08169000 on Texas Commission on Environmental Quality river segment 1811 station 12655. During a period of low springflow in the summer of 2011, late afternoon and early morning measurements of dissolved oxygen and temperature and presence of dinoflagellate blooms were monitored at six sites. Significant differences in diel fluctuations were found in all of these parameters among sites with and without the planktonic blooms. These fluctuations increased risk of hypoxia and hyperthermia conditions at sites of planktonic bloom events. Arrays of in-situ continuous monitoring temperature/light probes were used inside and outside of blooms. Wildlife and human health implications are that hypoxia and hyperthermia are known to promote conditions favorable to harmful microbes which may be transported from springs to coastal bays. In-situ data demonstrated that T. intermedium blooms, hypoxia, and hyperthermia occurred in the upper Comal headwaters. These natural environmental stressors may be avoidable if adequate springflows are maintained to buffer against these impacts.