Coastal and shallow lakes are often subjected to eutrophication due to nutrients from catchment farming activities. Lake Ellesmere (Te Waihora) is a hyper-eutrophic lake which has gained recent attention because of concerns over its ecological health and fishery status. This study investigated the benthic ecology of the lake by extensive spatial and temporal sampling. Eight littoral sites were sampled on a single occasion, and 20 benthic sites were sampled once per season for one year. Water chemistry conditions, substrate and invertebrate communities varied significantly around the lake. Salinity, pH, DO and seston were primarily affected by freshwater inputs from inflow streams and salt water intrusion due to the lake opening to the sea. On these occasions, salinity reached 32 ‰ at the lake outlet. The lake invertebrate community was depauperate, comprising of only two species of invertebrate predators restricted to the littoral zone and eight benthic invertebrate taxa, dominated by oligochaetes, amphipods and chironomids. Benthic invertebrate abundances also reflect the dominant local substrate, where oligochaetes and chironomids preferred areas of silt substrate, whereas Potamopyrgus preferred harder substrate. Stable isotope and gut analysis determined that the primary food sources within the lake were phytoplankton and algae. Macrophytes provided a minimal contribution to the food web, possibly relating to the change in status from a clear water, macrophyte dominated lake to a turbid, phytoplankton dominated condition since the Wahine Storm in 1968. Isotope analysis also showed that the lake food web was markedly different in its carbon values from food webs of its inflow streams and nearby marine source. However the lake food web did show a marine-derived carbon signature. A mesocosm experiment testing the effect of common lentic predators on the abundance of the lake chironomid Chironomus zealandicus, showed that if invertebrate predators were present in the lake they could markedly reduce the abundance of the pest prey species. This study highlights that the frequent re-suspension of bottom sediments, lake level fluctuation resulting in wetting and drying of littoral zones, and the management of the lake opening to the sea all have an effect on the benthic ecology of Te Waihora.