Ponds have been identified as biodiversity ‘hotspots’ that play an important role in supporting and maintaining biodiversity. In freshwater ecosystems, zooplankton are an essential trophic link between algae and fish, and some species act as biological indicators for aquatic system ‘health’. Most research pertaining to zooplankton biodiversity and community assemblages is skewed towards large lakes, reservoirs or urban ponds, while research on small ponds in rural environments is scarce. Consequently, the aim of my research was to examine and compare the biodiversity and community composition of zooplankton in natural ponds and dams in rural environments. To achieve this, 19 farm dams and 19 natural farm ponds in the Waikato region, New Zealand, were sampled for zooplankton in winter/spring (Aug-Sep 2018) and summer (Jan 2019). Environmental factors also were measured, including water temperature, dissolved oxygen, conductivity, water colour (gilvin), pH, chlorophyll-a, nutrient concentrations (total nitrogen and phosphorus), elevation, pond surface area and the number of waterbodies within a 2 km radius. All ponds were eutrophic to hypertrophic, and genera typical of these environments, such as Brachionus, Keratella and Polyarthra, were common in both farm dams and natural ponds. Zooplankton species richness was similar among farm dams and natural ponds (20.7 and 22.4 species, respectively; t-test p = 0.406), although there was a lot of variation within each pond type. Temperature (stepwise linear regression R² = 0.26; p = 0.025) and pond surface area (stepwise linear regression R² = 0.23; p = 0.016) were significant predictors of species richness in natural ponds; however, no significant relationships could be found between the measured environmental variables and species richness for farm dams. Zooplankton community composition differed between farm dams and natural ponds (one-way ANOSIM p = 0.014). A SIMPER analysis indicated that crustaceans (e.g., Chydorus sp., Acanthocyclops robustus and Simocephalus vetulus) were generally more abundant in natural ponds than in farm dams, whereas rotifers (e.g., Polyarthra dolichoptera and Keratella tecta) were more abundant in farm dams than in natural ponds. A canonical correspondence analysis indicated that variation in zooplankton community composition among natural ponds was explained by dissolved oxygen concentration (p = 0.002) and conductivity levels (p = 0.020). In contrast, the community composition of zooplankton in farm dams could not be explained by any of the measured environmental variables. Two genera (Erignatha clastopis and Octotrocha speciosa) and one species (Cephalodella theodora) were recorded that had not previously been identified in New Zealand. In total, three non-indigenous species were recorded in 7% of farm dams and 2% of natural ponds studied. My findings suggest that zooplankton communities differ between farm dams and natural ponds. Farm dams are primarily composed of a relatively unstructured subset of small, eurytopic and opportunistic zooplankton species (e.g., of Brachionus and Keratella). On the other hand, natural pond assemblages consisted of larger zooplankton species that are better adapted to the local conditions (e.g., Chydorus sp. and Simocephalus vetulus). This suggests natural ponds have had a longer period of time for more slowly dispersing species to colonise, whereas farm dams contain species that are capable of dispersing at much faster rates. Further, my results highlight that when examining environmental determinants of zooplankton community composition in water bodies across the landscape, natural and constructed ponds should be separated, as they appear to be structured by different variables. The prevalence of non-indigenous species in farm dams appears low relative to lakes and urban ponds in New Zealand, likely due to limited movement between ponds by humans. This suggests that these waterbodies are not acting as ‘stepping stones’ for non-indigenous species across rural landscapes. Overall, my research highlights the diverse taxa found in small agricultural ponds, and improves our knowledge and understanding of zooplankton communities in small natural and constructed ponds. Further, these findings emphasize the need for management and conservation of small water bodies, as they play a significant role in maintaining and supporting zooplankton communities (including rare species).