Escherichia coli (E. coli) first-order decay rates ranging from 3.34 to 11.9 d−1 (25–75% data range, N = 128) were recorded in two outdoor pilot-scale (0.88 m3) high rate algal ponds (HRAPs) continuously fed primary domestic wastewater over two years (influent E. coli cell count of 4.74·106 ± 3.37·106 MPN·100 mL−1, N = 142). The resulting removal performance was relatively constant throughout the year (log10-removal averaging 1.77 ± 0.54, N = 128), apart from a significant performance drop during a cold rainy period. E. coli removal performance was not strongly correlated to any of the meteorological or operational parameters recorded (e.g. sunlight intensity, pH, temperature). Hourly monitoring of E. coli cell count evidenced that E. coli removal, pH, dissolved oxygen (DO) and pond temperature peaked in the late afternoon of sunny summer days. Such improved daytime removal was, however, not evidenced in spring, even under sunny conditions causing milder increases in pH, DO and temperature. Overall, the data confirm the potential of HRAPs to support efficient E. coli removal during secondary domestic wastewater treatment and suggests E. coli decay was mainly caused by dark mechanisms episodically enhanced by indirect sunlight-mediated mechanisms and/or high pH toxicity.