The hydrodynamics in Lake Naivasha, a shallow endorheic lake, are simulated using the Delft3D Flow Module to investigate the major driving forces of hydrodynamics in the lake. The results showed wind as the major forcing. The shallow zones of the lake showed currents movement in the same direction as the wind while the deep zones showed currents movements against the wind direction. These findings were confirmed and further explained using an idealized model. Limited exchange between the Crescent Lake (crater lake which is temporally separated from the lake during low water levels) and the main lake was observed. These findings can explain the spatial variability of the water quality in the lake. Similar studies could be used in exploratory studies of the spatial-temporal variability in water quality in other shallow water systems.