The abundance and biomass of phytoplankton and ciliate taxa in lentic fresh waters were related to their resources, physicochemical conditions, potential consumers and water body type in 45 water bodies ranging from deep oligotrophic lakes to swamps, ponds and estuarine wetlands in South Island, New Zealand. Distinct phytoplankton assemblages were related to each water body type. Phytoplankton genera were positively related most strongly to dissolved reactive phosphorus concentrations, and also related positively to the biomass of ciliate consumers. The biomass of ciliate taxa was higher in swamps and ponds than other water body types. Biomass of the ciliate taxa: oligotrichs, prostomatids and Strombidium, was related strongly and positively to the biomass of their phytoplankton resource, and less strongly related to metazooplankton predators: calanoid copepods and Ceriodaphnia dubia. Our findings suggest that resource availability (bottom-up drivers) may be stronger determinants of phytoplankton and ciliate community composition than consumers (top-down effects).