Freshwater organisms are often exposed to contaminants such as heavy metals from stormwater discharges, which are dependent on rainfall duration and intensity. Therefore, standardized (48‐ or 96‐h) continuous exposure methods developed for whole effluent toxicity (WET) testing might not always accurately convey the effects of stormwater and runoff contaminants. The present study characterized the acute toxicity of copper (Cu), zinc (Zn), and cadmium (Cd) to freshwater amphipods (Hyalella azteca) and cadmium (Cd) to water fleas (Ceriodaphnia dubia) using a modified exposure design that integrated relevant pulsed durations and included post‐exposure monitoring. Less than 24‐h‐old C. dubia and 7 to 8‐day‐old H. azteca were exposed to water spiked with Cu, Zn, or Cd using 6‐, 12‐, 26‐, or 96‐h durations under standard laboratory conditions and monitored for cumulative mortality and reproduction (C. dubia only). Lethal effect (LC10s, LC25s, LC50s) and reproductive effect (EC25s, EC50s) were determined based on either mortality or reproduction of organisms at the end of each pulse (6, 12, or 26 h) and at the end of their respective tests (96 h). For all metals exposed to each organism, acute toxicity was found to be highest for the (96 h) continuous exposures. For pulsed exposures, mortality continued to increase following transfer to clean water for post‐exposure monitoring. These results indicate a latent effect of Cu, Zn, and Cd to H. azteca and Cd to C. dubia. The present study concluded that using the continuous (48‐ or 96‐h) WET exposure method overestimates the effects of stormwater and runoff contaminants. However, pulsed exposures without post‐exposure monitoring also underestimate the toxicity of contaminants. The proposed pulsed exposure design provides a compromise that is more realistic than current WET methods to assess impacts from episodic events and accounts for potential latent effects that may be overlooked without monitoring post‐exposure. Environ Toxicol Chem 2022;41:2488–2499. © 2022 SETAC