Long-term records of zooplankton distribution and abundance are increasingly being used as indicators of climate change. The North Atlantic, because of the 80 years of Continuous Plankton Recorder (CPR) surveys, is well-represented with such time series. However, there are few long-term data sets from the Pacific Ocean and especially from Antarctica, where traditional plankton sampling is logistically challenging. Here we test an alternative sampling method, the primary filter (PF) of the Scott Base reverse-osmosis (RO) desalination plant, which had the same mesh size (100 µm) as our standard plankton tows. We show, by qualitative comparison to fresh plankton samples collected with a plankton net, that the PF collects a representative zooplankton community, does not damage delicate or fragile forms (e.g., appendicularians, ctenophores, medusae, chaetognaths, pteropods, polychaetes, embryos with intact fertilization membranes, pilidia, bipinnaria), and that the large volumes of seawater filtered allow collection of rare meroplankton members. We further show that seasonal changes can be detected in the zooplankton when PF samples are fixed in formalin for later analysis. Desalination plant PFs may provide an innovative solution to study temporal patterns in the Antarctic zooplankton and have the potential to provide long-term data sets from other poorly sampled regions.