Lake Ellesmere/Te Waihora is one of New Zealand’s largest coastal, brackish water lakes. It has nationally significant wetland bird populations and is regionally important for iwi. The lake regularly experiences fluctuations in water level, resulting in a continually expanding and contracting littoral zone. This study investigated the impacts of these water level changes on the ecology of the lake. Water chemistry results collected over 12 months, confirm the lake is hypertrophic, due to high nutrient (nitrogen and phosphorus) concentrations resulting in high chlorophyll a levels and low water clarity. Water chemistry conditions were collected at five locations around the lake and showed marked spatial variation, with the eastern most end (Kaituna Lagoon) having generally the best water quality and lowest salinity (mean 4.9 ppt). Mean concentrations of total nitrogen ranged from 1.63 to 2.4 mg/L, chlorophyll a from 50 to 148 ug/L and total suspended solids from 151 – 248 mg/L. Seasonally, highest nutrient concentrations (mean, total nitrogen = 2.625 mg/L, dissolved reactive phosphorus = 0.059 mg/L and total phosphorus = 0.365 mg/L) occurred in late summer months (February – March), slightly decreasing but remaining high throughout winter. The benthic invertebrate community was surprisingly diverse, Crustacea (Paracorophium excavatum), Oligochaeta, Mollusca (Potamopyrgus antipodarum) and Chironomidae (Chironomus zealandicus) were dominant community members in the littoral zone, although 24 other taxa were collected. At high water levels, taxonomic richness increased in the eulittoral zone, while decreasing in the mid-littoral and lower littoral zones. In contrast, density decreased with higher water level in the eulittoral and mid-littoral zones, while increasing in the lower littoral zone. Benthic invertebrate communities appeared to be adapted to periods of intermittent dewatering, and even sustained dewatering under cooler temperatures. Despite the relatively high diversity of benthic invertebrates, invertebrate predators are generally absent from the lake. My results suggest multiple factors and interactions from predation pressure, salinity and lack of macrophytes are likely responsible for the absence of predatory invertebrates such as damselfly (Xanthocnemis zealandica) and dragonfly (Procordulia grayi) larvae. The lack of significant relationships between water quality variables and water level, and the positive relationship between chlorophyll a and salinity, suggests that current lake opening events do not have a positive effective on either water quality or phytoplankton biomass in Lake Ellesmere/Te Waihora. However, the current lake opening regime seems to be favourable to benthic invertebrate survival in the littoral zone, as the lake is predominantly open over winter when temperatures are lower, reducing the risk of desiccation. Anthropogenic activities which modify hydrodynamic and water quality conditions can potentially have a large negative impact on the structure and diversity of the littoral invertebrate community as well as flow on effects through the lake food web. Based on results from this study, I suggest a minimum lake level at Taumutu of 0.6 m during the months from November – April in order to protect benthic invertebrate communities in the eulittoral zone from extensive loss of habitat, extreme temperature and reduced risk of desiccation. Having a minimum set at ~0.6 m would provide sufficient littoral zone habitat for the lakes extensive bird life and fish populations. In addition, immediate efforts are needed into reducing nutrient loads into the lake, through improved farm management (nutrient and stocking budgets) and riparian fencing. Furthermore, physical and chemical water quality properties would benefit from an increased water level over summer months, by reducing water temperatures, diluting readily available nutrient concentrations and potentially reducing phytoplankton (and potentially toxic cyanobacterial) blooms.