Missaghi, Shahram2014-10-302014-10-302014-07https://hdl.handle.net/11299/167393University of Minnesota Ph.D. dissertation. July 2014. Major: Water Resources Science. Advisors: Prof. Miki Hondzo Dr. Lorin Hatch. 1 computer file (PDF); ix, 139 pages.Morphologically complex lakes usually have a significant water quality heterogeneity and hydrodynamic gradients that require a three dimensional (3D) model to accurately capture their temporal and spatial dynamics. The objectives of this research were to evaluate and apply a 3D coupled hydrodynamic and ecological model to a morphologically complex lake and to investigate the effects of a changing climate on the lake ecosystem. The research was conducted in a series of four separate studies including modeling investigations and laboratory experiments. First, a 3D hydrodynamic model (ELCOM ) coupled with an ecological model (CAEDYM) was applied to three bays of the morphologically complex Lake Minnetonka, MN, to simulate water temperature, dissolved oxygen, total phosphorus, and algal concentrations. The 3D model was calibrated and validated in two different years, and model results compared well with extensive field data. Lake hydrodynamic and ecological processes were discovered to be sensitive to mixing due to inflow and wind variability over seasonal stratification. In the second study, two sensitivity and uncertainty analysis methods were applied to the model to evaluate uncertainties in the model predictions. The contributions of predicted water temperature, dissolved oxygen, total phosphorus, and algal biomass contributed 3, 13, 26, and 58% of total model output variance, respectively. A laboratory experiment was conducted to measure the influence of fluid motion on growth and vertical distribution of <italic>Microcystis</italic>in a Plankton Tower bioreactor. The laboratory results indicated that a depth-averaged energy dissipation rate in the range from 3 x 10-7 to 3 x 10-6 m2 s-3 facilitated <italic>Microcystis</italic> growth. Fourth, the applied calibrated and validated 3D model revealed the influence of local meteorological and global climate conditions on key water quality parameters and fish habitat in 3 bays of Lake Minnetonka. The research was conducted by simulating the model and analyzing the model output results under three climate scenarios of historical normal (HN), future (FU), and future extreme (FE). Water temperature (T) and dissolved oxygen (DO) concentrations were used to investigate the temporal and spatial variability of fish habitat dynamics. The epilimnetic water temperature of the FU and FE climate scenarios were up to 4 °C warmer than the HN scenario during ice-free seasons, stratification periods were predicated to expand up to 23% (46 days), and thermocline depth to increase 49% under the FE climate scenario. In all cases hypolimnion was mostly anoxic by June 15, but started by April 15, May 1, and May 15, under the three climate scenarios of HN, FU, and FE respectively. Under future scenarios the good growth, restricted growth and lethal coolwater fish habitats that were based on T and DO thresholds changed +16%, -18%, and +85% compared to the HN scenario. A modest change (8% of total lake volume) of good growth and restricted growth into lethal habitat separated the summer good growth coolwater fish habitat by over 3 weeks. The research brought out the need for a 3D analysis in capturing the significant water quality heterogeneities and the ecological hot spots in a morphologically complex lake.en3D modelingClimate changeFish habitatHydrodynamicSensitivity and uncertaintyWater qualityWater resources scienceThesis or Dissertation