Excess nutrient loading often promotes harmful algal blooms. Despite many past studies, few algal bloom control methods show clear, long-term improvements in water quality. For example, chemical treatments are often used to control algal blooms because they can cause large, rapid declines in algal abundance. However, these effects are often transient requiring future treatments that increase costs and risks to water quality. Moreover, empirical tests of repeated applications or combinations of different treatments are rare, even with their common use across industries, like aquaculture and drinking water. To rigorously test the effects of single or combined treatments on water quality in a eutrophic aquaculture pond, copper sulfate pentahydrate (henceforth called copper) and Phoslock were used independently (full dose) or combined (each at half dose) in a 56-day field experiment conducted in a hypereutrophic aquaculture pond. The two copper-containing treatments caused rapid declines (-83%) in algal abundance the day after treatment followed by very large (2,617%) increases after another five days. In contrast, zooplankton were reduced by 43% in the copper treatment but minimally affected (+1%) by the combined treatment the day after application. To further show that copper treatment is the mechanism responsible for the negative effects on zooplankton and phytoplankton, half of the mesocosms for all four treatments were treated with a full dose of copper on day 13 and similar effects on phytoplankton were observed as when copper was initially applied. The combined treatment was more effective at controlling phytoplankton than the copper only treatment, in part, because of lesser negative effects on zooplankton. Overall, this experiment further highlights the long-term, negative effects that chemical treatments, like copper, have on non-target taxa, such as beneficial zooplankton, which limits their potential for ecological and sustainable control of harmful algal blooms.