In San Diego Bay, marine organisms are exposed to non-point source stormwater effluent containing the contaminants of concern copper and zinc. United States Environmental Protection Agency (U. S. EPA) Whole Effluent Toxicity (WET) test methods were developed to evaluate the toxicity of continuous point source discharges. These tests are now applied to episodic stormwater discharges. There is concern that static or static-renewal WET methods are not representative the episodic, short-term nature of stormwater discharges. This study modified WET test methods to assess the relative toxicity of copper and zinc under three discharge scenarios, corresponding to the 50th , 75th, and 95th percentile of historical rainfall durations in San Diego. Pulsed contaminant studies were initiated with two common WET test species, the purple sea urchin (Strongylocentrotus purpuratus), and mysid shrimp (Americamysis bahia), representing chronic and acute toxicity test endpoints. To mimic San Diego rain events, laboratory assays were performed for copper and zinc individually and as mixtures at time durations of 3, 6, and 12-hours, followed by transfer to uncontaminated filtered seawater from San Diego Bay for the remainder of the traditional 96-hour WET testing period. LC⁵⁰ and EC⁵⁰ values were calculated for copper and zinc exposures at each time-point. Traditional 96-hour static reference toxicant tests were performed concurrently as a means to compare static exposure LC/EC⁵⁰ values to those found from pulsed toxicity tests. For both sea urchin and mysid shrimp, an increase in contaminant exposure time corresponded to increased toxicity, resulting in LC/EC⁵⁰ values up to two orders of magnitude greater than standard 96-hour tests. Copper and zinc mixtures elicited less than additive toxicity for all exposure regimes, suggesting that mixtures were less toxic than when exposed as single metal exposures for these contaminants. Exposure times used in standard WET testing likely overestimate the toxic effects of short-term episodic stormwater discharges influencing San Diego Bay. The results suggest that current WET testing protocols may be unnecessarily conservative for estimating episodic discharges toxicity.