The Standardized Aquatic Microcosm (SAM) was used to assess the effects and behavior of copper at the ecosystem level. The concentration of algal cells and Daphnia magna, pH, dissolved organic carbon (DOC), and dissolved and ionic copper concentration were measured for 489 d and used to explain the recovery sequence of a community of organisms. The results indicate that a resistant algal species was crucial for initiating the recovery sequence in these microcosms and that the timing of D. magna blooms was variable but highly correlated with decreasing ionic copper. In order to explain copper toxicity and the success of the recovery phase, a stepwise analysis of the functional role of the resistant algal species Oocystis pusilla, and the tolerance of D. magna was undertaken. These process studies determined that O. pusilla was a suitable food for D. magna, and that this algal species could also act as a major ligand for copper, although sorption was probably important only for a limited time during the bloom. These studies also concluded that copper bioavailability controlled toxicity because it was shown that D. magna from the microcosms exhibited no resistance to copper toxicity, even though the dissolved copper concentration was 5 times the LC50 value (concentration lethal to 50% of the population). DOC and pH, which were controlled by algal metabolism, were probably important for decreasing ionic copper, which allowed the recovery sequence to begin. Additional studies showed that the microcosm-derived DOC was able to complex copper at low pH and that DOC was highly correlated with reduced concentrations of ionic copper.