Zooplankton were collected from ten lakes in the Wellington Region in 2022, with a further three historic samples collected from 2019 (including one unique lake). These were used to explore community composition of these lakes, as well as trends in rotifer inferred TLI assessments, the proportions of native versus non-native zooplankton, and crustaceans versus rotifers. Based on these results, lakes can be ranked in the following order, from lowest to highest rotifer inferred TLI values; Lake Ngarara (1.8; oligotrophic), Lake Waitawa (3.9), Barton’s Lagoon (3.9; both mesotrophic), Turner’s Lagoon (4.0), Boggy Pond, (4.2), Waimanu Lagoon (4.5; all eutrophic), Lake Pounui (5.0), Lake Kohangatera (5.1), Matthew’s Lagoon (5.3; all supertrophic), Lake Waiorongomai (8.0) and Lake Nganoke (8.3; both hypertrophic). The Matthew’s Lagoon (both 5.3) and Lake Waitawa results (3.3 and 4.5) were averages of samples from two years. Nevertheless, these results should be treated with caution, due to being calculated from single samples, or samples from different years, rather than the recommended multiple samples collected over different seasons. Most of the lakes were devoid of non-native species. Nevertheless, Lakes Pounui and Waitawa both had populations of the introduced Daphnia galeata, which is native to northern hemisphere temperate regions (i.e., Holarctic), while Lake Waitawa also possessed a population of the Australian copepod Boeckella minuta. The latter record is interesting in that it is otherwise only known from constructed waters in New Zealand, including the Karori Reservoirs and Waikato Hydroelectricity Lakes. As such, this is the first record of this species established in a natural lake in New Zealand. The zooplankton community of Lake Pounui (98.7%), Lake Waitawa in 2019 (89.9%), Lake Waitawa in 2022 (76.7%) and Boggy Pond (73.1%) were heavily crustacean dominated, while Lake Kohangatera (5.9% crustaceans), Matthews Lagoon (23.5%), Lake Ngarara (27.9%), Lake Waiorongomai (28.6%), Barton’s Lagoon (30.5%), Lake Nganoke (32.6%) and Turner’s Lagoon (34.7%) were heavily rotifer dominated. Matthew’s Lagoon (52.1%) and Waimanu Lagoon (40.4%) had similar proportions of crustacean and rotifer zooplankton. The size distributions of zooplankton in Lakes Pounui and Waitawa are likely influenced by the crustacean invaders in these lakes. Different degrees of top-down control by zooplanktivorous fish, removing larger crustacean zooplankton, may influence the variability among the remaining waterbodies, though longer-term data and knowledge of fish communities is required to better determine this. Besides B. minuta, the waterbodies sampled included some unusual species. A Brachionus rotifer, with affinities to B. caudatus, was recoded from Lake Kohangatera and Boggy Pond; this seemingly represents an undescribed species. The typically estuarine copepod Gladioferens pectinatus and saline rotifer Brachionus plicatilis were recorded in Waimanu Lagoon, reflecting a probable marine influence in this lagoon. Gladioferens pectinatus was also recorded in Matthews Lagoon, representing a rare occurrence for this species in a freshwater lake.