The downwelling irradiance in water is highly variable due to the focusing and defocusing of sunlight and skylight by the wave-modulated water surface. While the time scales and intensity variations caused by wave focusing are well studied, little is known about the induced spectral variability. Also, the impact of variations of sensor depth and inclination during the measurement on spectral irradiance has not been studied much. We have developed a model that relates the variance of spectral irradiance to the relevant parameters of the environmental and experimental conditions. A dataset from three German lakes was used to validate the model and to study the importance of each effect as a function of depth for the range of 0 to 5 m.