The increasing frequency of Cyanobacterial blooms in freshwater bodies raise concerns around the globe. The consequences of this phenomenon impact not only human health but the entire surrounding ecosystem. During the past decades, numerical modelling has been increasingly used to investigate and study aquatic systems. Hydrodynamic and Ecological models are developed in parallel to simulate processes, evaluate potential remedies, and investigate future scenarios. This project aimed at developing a 3D hydrodynamic and water quality (ecological) model to assess the eutrophication conditions of Lake Vomb under current and future scenarios. MIKE 3 FM software was used in the analysis with meteorological, hydrological, and water quality data. The hydrodynamic model performance was satisfactory in terms of water temperature simulation with root-mean-square-error (RMSE) ranging between 0.38-1.2 oC. In the ecological model, Chlorophyll-a (Chl-a) was simulated as a surrogate for Cyanobacteria. The model was adequate in simulating Chl-a concentrations with a Nash-Sutcliffe efficiency (NSE) of 0.94 during calibration and 0.84 after validation. The results showed that Lake Vomb’s nutrient concentrations are highly influenced by external nitrogen loading and internal phosphorus loading. The results also showed that Chl-a levels are correlated with the total phosphorus levels in the lake. Future water quality projections were attempted through two Representative Concentration Pathways (RCPs) for the year 2050. The projections utilized only changes in air temperatures and precipitations and suggested significant increase in Cyanobacteria biomass independence of changes in external nutrient loading.