Few studies have examined microfaunal assemblages living among Salix cinerea infestations in freshwater wetlands, or their responses to willow control treatment. The aim of this research was to quantitatively examine microfaunal assemblage abundance, richness and community composition among S. cinerea stands within the South Taupo Wetland, and determine whether these microfaunal assemblages are affected by willow growth and willow control treatment. Long-term effects of microfaunal community composition between native vegetation versus live and dead S. cinerea were examined in two blocks of the Waiotaka Scenic Reserve. Microfauna and physicochemical sampling were performed on three occasions to assess any seasonal effects on community composition. Results indicated there were no significant differences of physicochemical variables amongst natives, live and dead S. cinerea, with the exception of dissolved oxygen in late summer and canopy density in all seasons. This could be due to the S. cinerea trees representing stand-alone individuals, with a continuous canopy not yet formed. Overall, apart from shading and dissolved oxygen levels, environmental conditions of S. cinerea stands in this study seemingly made no significant difference to environmental variables. The abundant taxa found in the study were copepods, cladocerans and ostracods along with diverse species of rotifers, including the first record for New Zealand of the rotifer species Tetrasiphon hydracora. ANOVA indicated that there were no significant differences in microfaunal species richness between native, live and dead S. cinerea in any season. However, MDS ordination and ANOSIM results of species composition indicated that microfaunal assemblages were clustered in groups either side of the sand bar, suggesting that Blocks 1 and 2 functioned independently. This may be influenced by hydrological differences between Block 1 and 2 of the wetland reserve, with differing responses to fluctuating lake levels and seasonal rainfall, suggesting that microfaunal communities are regulated by hydrology rather than by the presence of willows or willow control. Short-term effects of microfaunal community composition post willow control treatment were examined in Block 2 of the Waiotaka Scenice Reserve. Microfauna and physicochemical sampling were performed before and after treatment to assess effects on community composition post willow control treatment, using ground control method of drill and inject with a herbicide mix of metsulfuron. No significant differences in environmental variables were observed post treatment, with the exception of canopy density cover. Treated S. cinerea trees died and lost their leaves after ground application of metsulfuron. Microfaunal abundance and diversity were low before and treatment, suggesting that the application of metsulfuron made little difference to microfaunal assemblages. Overall, the findings of this study indicate that the presence of S. cinerea seemed to make no significant difference to microfaunal abundance and diversity, possibly due to stand alone individuals rather than the formation of a dense canopy. Furthermore, ground control treatment of S. cinerea using metsulfuron had no direct or indirect impacts to microfaunal abundance and diversity. However, had the study been undertaken under a dense canopy of S. cinerea it is likely that the results may potentially be different.