Most of what is known about the effects of ocean acidification on zooplankton relates to a few species composed of calcium carbonate, or comes from laboratory and mesocosm studies that observe a relatively small number of species, primarily copepods. So far little is known about how entire zooplankton communities may change due to elevated carbon dioxide levels. We examined changes in zooplankton residential to coral reefs at two reefs in Papua New Guinea where underwater seeps create a natural pH gradient. Traditional net tows, emergence traps, and acoustical instruments were used to collect and observe zooplankton over three separate seasons and emerging from different types of substrata. All methods indicated a dramatic loss in zooplankton abundance where pH was reduced to 7.8 compared to healthy reefs with a normal pH of 8.1. We observed both changes in the overall zooplankton community, and examined each taxonomic group separately to investigate differences in the sensitivity between taxonomic groups. Reduced quantities of zooplankton will likely affect marine organisms that feed on them.