This report describes a modelling and remote sensing study of lakes Onoke and Wairarapa that seeks to determine water quality and ecological effects of specific management scenarios, and therefore inform the Ruamāhanga Whaitua Committee of potential water quality management options for lakes Onoke and Wairarapa. The study applied both one dimensional (1-D) and three dimensional (3-D) ecologically coupled hydrodynamic models to simulate current and scenario-based water quality variables. The Baseline model (calibration) simulates “current conditions” including management practices between 1992 and 2014. Business As Usual (BAU), SILVER and GOLD scenarios were all run using representative data catchment inflow and nutrients for mitigation taking effect in 2025, 2040 and 2080. Additional hydrodynamic scenarios were modelled (which also include catchment mitigations above). They were: deepening both lakes by 1 m, Ruamāhanga diversion back into Lake Wairarapa, and Lake Onoke summer outlet closed scenarios. These scenarios were provided by the Ruamāhanga Whaitua Committee. Within Lake Wairarapa, catchment mitigation-based scenarios showed considerable potential for the improvement of water quality. These mitigations simulated that the trophic state of the lake could change from the current supertrophic category, to the top of the eutrophic category (GOLD and SILVER mitigations). However, this still indicates poor water quality and high turbidity/low water clarity. In addition, these catchment mitigations did not move the lake from a NOF D category for total phosphorous (TP). Simulations indicated that larger reductions in TP (60%) (with SILVER2080 mitigations of other nutrients) could achieve a NOF C category for TP. Simulations that included the re-establishment of macrophytes also indicated NOF C category for TP (under SILVER2080), however only under a 1 m depth increase scenario, and under Ruamāhanga diversion scenario. These simulations indicated that the trophic status could move to the mid-eutrophic category. However, this is still indicative of poor water quality. Catchment scenarios had a greater influence on Lake Onoke trophic status compared to Wairarapa, due to the shorter residence time and low internal load (from the sediments) relative to external load. In effect, the composition of Onoke aligns closely with that of its inflows. Water quality in Lake Onoke is susceptible to changes in water quality in Lake Wairarapa, particularly in relation to chlorophyll a (chl a) and total suspended solids (TSS). High sediment resuspension events in Lake Wairarapa transport increased levels of suspended sediment to Lake Onoke. The very low residence time in Onoke does not allow adequate time for significant phytoplankton growth within the lake. However, 3-D simulations show higher phytoplankton concentrations at times in the western lake, relating to flushing and transport effects. The outlet-closed scenario in Lake Onoke simulated increased water quality in both 1-D and 3-D models However, we note that the risk of cyanobacteria blooms was low, but marginally increased. Also 1-D models suggested that the simulated TLI under SILVER2080 was almost identical to outlet closed SILVER2080. The 3-D model simulated lower chlorophyll concentrations and higher TSS under SILVER2080 outlet closed (compared to SILVER2080 and Baseline), largely due to changes in hydrodynamics and flushing. Therefore, these results show no conclusive evidence that water quality would be significantly increased or decreased in comparison to SILVER2080 under an outlet closed scenario. However, we note that in situ monitoring and expert opinion has indicated that under outlet closed conditions the lake is more susceptible to eutrophication.