In this paper, for the first time, all five Great Lakes are simulated using a 3D baroclinic model using a single, seamless unstructured mesh without nesting, including adjacent flood plains and watershed inflows to better connect the hydrodynamic model to the hydrologic model. The hydraulic controls at Sault St Marie and Niagara Falls are simulated using an internal flow boundary approach with the observed flow. The model is shown to exhibit good skills for total water level (TWL) and temperature, with RMSE of 9.5 cm for TWL and similar to 1.6 degrees C for surface temperature and temperature profiles from a 60-day simulation. Sensitivity results reveal the importance of hydrologic forcing even for this short-term simulation. Results from a 210-day simulation indicate that the model is capable of capturing major lake-wide circulation patterns discussed in previous studies and providing further details in those patterns. The new model can potentially serve as a base to unify Great Lakes modeling while simultaneously providing flexibility for site specific studies in any areas of interest.

Since the late 1990s, the Laurentian Great Lakes have experienced persistent low water levels and above average over-lake evaporation rates. During the winter of 2013-2014, the lakes endured the most persistent, lowest temperatures and highest ice cover in recent history, fostering speculation that over-lake evaporation rates might decrease and that water levels might rise. To address this speculation, we examined interseasonal relationships in Lake Michigan's thermal regime. We find pronounced relationships between winter conditions and subsequent fall heat content, modest relationships with fall surface temperature, but essentially no correlation with fall evaporation rates. Our findings suggest that the extreme winter conditions of 2013-2014 may have induced a shift in Lake Michigan's thermal regime and that this shift coincides with a recent (and ongoing) rise in Great Lakes water levels. If the shift persists, it could (assuming precipitation rates remain relatively constant) represent a return to thermal and hydrologic conditions not observed on Lake Michigan in over 15years.

Hypoxia within lower Green Bay has been a problem for decades, and the problem may be worsening. Numerical modeling and field studies are underway to improve our understanding of circulation, thermal regime and anoxia in Green Bay. Model validation was successful because modeled currents are reasonably close to data collected at three monitoring stations. Model results showed that wind shear and circulation are stronger in winter than in summer. Water exchange between Lake Michigan and Green Bay is stronger during the summer, when wind shear is mostly axial. Mass exchange affects stratification, and possibly the development of anoxia. Results showed stable anticyclonic gyres both south and north of Chambers Island, and cyclonic gyres near the mouth of the Fox River and south of the passages between Green Bay and Lake Michigan. The former is consistent with the Fox River plume clinging to the east shore of the bay.

The influence of suspended sediments on the Lake Michigan ecosystem was examined using a 3-dimensional (3-D) coupled biological and physical model developed by Chen et al. (part I). The model was driven by the realistic meteorological forces observed in March 1998, with daily inputs of suspended sediment concentration that were derived from temporally and spatially interpolated satellite imagery. The model results show the significant impact of a seasonally recurring coastal resuspension plume on the spatial and temporal variation of the nutrients and plankton in southern Lake Michigan. The plume-released nutrients played an essential role in maintaining the nutrient level in the lake. Although the growth of phytoplankton in the plume depended on the availability of nutrients and light, the offshore decrease in phytoplankton biomass still satisfied the Sverdrup's relationship. Cross-shore fluxes of nutrients and phytoplankton were controlled by episodic wind events with a period of ≈5–7 days: offshore during southward winds and onshore during northward winds. The flux estimates for biological variables suggest that the microbial food web is a key contributor to secondary production in southern Lake Michigan and the lower trophic level food web system could be dynamically divided into two decoupled loops: (1) detritus–bacteria–microzooplankton–large zooplankton; and (2) nutrient–phytoplankton–detritus. The model-predicted spatial distributions of nutrients and phytoplankton were in reasonable agreement with observations taken during the 1998 EEGLE interdisciplinary cruises, suggesting that the model was sufficiently robust to capture the basic characteristics of the Lake Michigan ecosystem during the plume event.

A three-dimensional primitive equation numerical ocean model, the Princeton model of Blumberg and Mellor (1987), was applied to Lake Michigan for the 1982-1983 study period. The model has a terrain following (sigma) vertical coordinate and the Mellor-Yamada turbulence closure scheme. This two-year period was chosen because of an extensive set of observational data including surface temperature observations at permanent buoys and current and temperature observations from subsurface moorings. The emphasis of this paper is on the large-scale seasonal variations of thermal structure and circulation in Lake Michigan.The hydrodynamic model of Lake Michigan has 20 vertical levels and a uniform horizontal grid size of 5 km. The model is driven with surface fluxes of heat and momentum derived from observed meteorological conditions at eight land stations and two buoys from April 1982 to November 1983. The model was able to reproduce all of the basic features of the thermal structure in Lake Michigan: spring thermal front, full stratification, deepening of the thermocline during the fall cooling, and finally an overturn in the late fall. The largest currents occur in the fall and winter when temperature gradients are lowest and winds strongest. Large-scale circulation patterns tend to be cyclonic (counterclockwise), with cyclonic circulation within each subbasin. All these facts are in agreement with observations.

Combined use of remote sensing in the visible, infrared and microwave spectral regions, direct in situ measurements and model numerical experiments makes it possible to study inland water bodies as elements of water body-catchment-atmosphere-systems with good spatial and temporal resolution. In this paper examples are presented of the remote sensing methods developed for detection of hydrodynamics of large water bodies (e.g. frontal and upwelling zones, internal waves, warm and cold surface layers), monitoring of chlorophyll concentration, suspended minerals and dissolved organic matter (DOM) in lakes, mapping of shallow water zones, wetlands and landscape structures, monitoring of ecological condition and changes of drainage basins, and studying the state of the atmosphere over lakes and catchment areas.

The results of numerical modelling of large-scale circulation in Lakes Onega and Ladoga are presented, with primary emphasis on the temporal variability of currents with time scales of days. Some typical circulation patterns have been inferred from model calculations. They reflect the existence of different dynamic regimes in the lakes, namely, forced and free circulation regimes. The forced circulation regime is the well-known wind-induced double-gyre circulation accompanied by coastal upwelling and downwelling. A case of double-gyre circulation in Lake Onega was investigated in particular detail. The second dynamic regime is a free response (or a relaxation) of the stratified lake to wind cessation, and is connected closely with the evolution of wind-induced upwelling and thermal front propagation. Diagnostic calculations demonstrate that the regime of relaxation supports the restoration of cyclonic circulation in Lake Onega. Barotropic circulation patterns in Lake Ladoga were calculated with the emphasis on prevailing winds from west to south-east. Our calculations show that the bottom relief of Lake Ladoga causes asymmetry in the double-gyre circulation patterns. In particular, approximately equal cyclonic and anticyclonic circulation cells appearing in the case of southerly wind transform to a single dominant cyclonic cell and several small anticyclonic cells in the case of westerly wind. We also found especially strong sensitivity of the sense of rotation of the largest gyre to the east-west components of the wind vector.