This study presents the Lake Okeechobee Environment Model (LOEM), a three-dimensional (3D) hydrodynamic, sediment, water quality, and submerged aquatic vegetation (SAV) model of Lake Okeechobee, Florida. The LOEM is developed under the framework of the EFDC model (Hamrick 1992). Lake Okeechobee is the largest subtropical lake in North America (1,730 km²), it is very shallow (mean depth 2.7 m), and it includes a littoral habitat that makes up 20% of its area. The LOEM is calibrated, verified, and validated to 3 years of water quality and SAV data. The water quality results are consistent with observed data from 25 locations in the lake. The model is capable of reproducing key water quality characteristics of the lake without having to resort to extensive, site-specific parameter manipulations. The SAV model is calibrated using measured SAV data in the lake. The SAV model is capable of representing the spatial and temporal variations of SAV variations in the lake well. The LOEM is applied to study water quality and SAV processes in the lake. The model results are consistent with observed data indicating that algal growth in the lake is primarily nitrogen limited in the summer and nitrogen and light co-limited in the winter. Lower water elevation generally leads to larger SAV area. SAV can have positive impact on the lake water quality by reducing algae concentration. The calibrated, verified, and validated LOEM model serves as a useful tool to support lake management.