Aim Constructed water bodies (e.g. water supply and hydroelectricity dams, ornamental ponds) are invaded at faster rates than natural waters, but the mechanisms that lead to this pattern are uncertain. We aimed to determine whether constructed lakes have lower zooplankton species richness or differ in species composition relative to natural waters, which might allow them to be invaded more readily. Location North Island, New Zealand. Methods Sediment cores were collected from 23 natural and 23 constructed lakes, ponds and reservoirs. Zooplankton diapausing eggs were hatched from sediments to assess species composition and richness. Results Average species richness between natural and constructed water bodies was not significantly different. Stepwise linear regression indicated latitude and maximum depth were significant predictors of species richness in natural waters (P = 0.002 and 0.016, respectively). No significant predictors were elucidated for constructed waters. Species in natural waters consisted mainly of planktonic species, while assemblages in constructed waters were more varied, comprising of more littoral and benthic species, and included many species recorded from only single water bodies. Canonical correspondence analysis indicated that trophic state explained the greatest proportion of variation in species composition of natural waters (P = 0.002). Distance to nearest water body and number of water bodies within a 20 km radius (i.e. opportunity) explained the greatest proportion in constructed waters (P = 0.040 and 0.038, respectively). Main conclusions Natural and constructed waters had similar species richness per water body, but community composition varied between them. The core group of species found in natural waters are better adapted to pelagic conditions, and may therefore be better at reducing establishment rates of new arrivals than assemblages in constructed water bodies, which had more varied assemblages. Our study suggests that manipulating new water bodies, so that they develop mature communities faster, may reduce establishment rates of non-indigenous species.