In agricultural landscapes, free-water surface flow wetlands (FWS) are constructed mainly to improve water quality; however, their contribution to biodiversity conservation is increasingly recognised. To inform biodiversity management in FWS treating agricultural runoff, we surveyed the vegetation and fauna assemblages in five established FWS in a lowland, pastoral landscape in the central North Island, New Zealand. The FWS had been established for between 3 and 19 years, planted with a restricted range of native plant species, and fenced to exclude livestock access. Larger wetlands hosted significantly more plant and mammal species. However, other than wetland size, we found few other significant relationships between wetland habitat, landscape characteristics, and measures of biodiversity (total species, proportion of native species, number of wetland specialists, or threatened species). We recorded one-hundred and thirteen plant, twenty bird, five mammal, eighty-five terrestrial invertebrates, forty-seven aquatic invertebrates, six fish, and two amphibian species inhabiting the FWS. Native species comprised 96% of the total aquatic invertebrate fauna identified. For other taxa, native flora and fauna accounted for half or less than half of all species identified: 53% terrestrial invertebrates, 50% fish, 45% birds, 32% plants, and 0% amphibian and mammal species. Few wetland specialists (aquatic or wetland-adapted) or threatened native species were detected, probably reflecting the limited range of wetland plant species in initial plantings and the difficulties native taxa face when colonising new habitat where potential reservoirs of colonist species are also depauperate or too distant. FWS support native biodiversity, but further enhancements may require active management of exotic and pest species to minimise competition or predation on native species.