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Understanding and modeling water quality in a lake/reservoir is important to the effective management of aquatic ecosystems. The advantages and disadvantages of different water quality models make it challenging to choose the most suitable model; however, direct comparison of 1-D and 3-D models for lake water quality modeling can reveal their relative performance and enable modelers and lake managers to make informed decisions. In this study, we compared the 1-D model MINLAKE and the 3-D model EFDC+ for water temperature, ice cover, and dissolved oxygen (DO) simulation in three Minnesota lakes (50-m Carlos Lake, 23.5-m Trout Lake, and 5.6-m Pearl Lake). EFDC+ performed well for water temperature and DO simulation in the open water seasons with an average root mean square error (RMSE) of 1.32 °C and 1.48 mg/L, respectively. After analyzing the ice thickness with relevant data, it was found that EFDC+ calculates a shorter ice cover period and smaller ice thickness. EFDC+ does not consider snowfall for ice thickness simulation. The results also revealed that EFDC+ considers spatial variance and allows the user to select inflow/outflow locations precisely. This is important for large lakes with complex bathymetry or lakes having multiple inlets and outlets. MINLAKE is computationally less intensive than EFDC+, allowing rapid simulation of water quality parameters over many years under a variety of climate scenarios.