AbstractA fast and effective microwave treatment procedure was developed for the ADDA–enzyme‐linked immunosorbent assay analysis of total extracellular and intracellular microcystins and nodularins in drinking water and ambient water. This microwave treatment procedure for a full batch of samples required 10–20 min versus the 3–4 hr typically needed for three freeze/thaw cycles. The obtained lowest‐concentration minimum reporting level and method detection limit were 0.21 and 0.09 μg/L microcystin‐LR (MC‐LR) equivalents, respectively. Mean recoveries of 80%–92% with relative standard deviations of 4.2%–9.0% were obtained for all studied water matrices fortified at concentrations of 0.3–2.0 μg/L MC‐LR. Compared with US Environmental Protection Agency Method 546, this alternate procedure provided more effective cell lysis and subsequently detected significantly higher concentrations of total microcystins and nodularins in a few water samples collected during harmful algal blooms, such as 61.0 versus 34.4 μg/L MC‐LR equivalents in Lake Erie and 11.5 versus 9.1 μg/L MC‐LR equivalents in an Indiana reservoir.