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The Jim Bertram Lake System consists of several stream impoundments within the City of Lubbock, Texas (USA). Baseflow in the upstream reach is dominated by nitrogen-rich-treated wastewater. While toxic blooms of Prymnesium parvum have occurred in this system for ∼2 decades during fall or winter-spring, little is known about water quality variables that facilitate blooms or the alga’s spatiotemporal distribution. Water quality associations were examined monthly over a 1-year period. Total phosphorus was largely below the detection limit, suggesting that the system is phosphorus limited. Algal abundance was low during the assessment period and associations were determined using multiple logistic regression. Algal incidence was negatively associated with temperature and positively with organic nitrogen and calcium hardness. These findings conform with earlier reports but positive associations with the latter two variables are noteworthy because they have not been widely confirmed. Spatiotemporal distribution was evaluated in fall and winter-spring of three consecutive years. Prymnesium parvum incidence was higher in the upper than in the lower reach, and detections in the lower reach occurred only after a dense bloom developed in the upper reach contemporaneously with stormwater runoff-associated flooding. Thus, the upstream reach is a major source of propagules for downstream sites. Because urban runoff is a source of phosphorus and its nitrogen: phosphorus ratio is lower than prevailing ratios in the upper reach, what triggered the bloom was likely relief from phosphorus limitation. This study provided water quality, geographic and hydrological indices that may inform prevention and control methods for harmful algae in nitrogen-enriched urban systems.