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In this letter, we explore the effectiveness of a novel regression method in the context of the estimation of biophysical parameters from remotely sensed imagery as an alternative to state-of-the-art regression methods like those based on artificial neural networks and support vector machines. This method, called Gaussian process (GP) regression, formulates the learning of the regressor within a Bayesian framework, where the regression model is derived by assuming the model variables follow a Gaussian prior distribution encoding the prior knowledge about the output function. One of its interesting properties, which gives it a key advantage over state-of-the-art regression methods, is the possibility to tune the free parameters of the model in an automatic way. Experiments were focused on the problem of estimating chlorophyll concentration in subsurface waters. The achieved results suggest that the GP regression method is very promising from both viewpoints of estimation accuracy and free parameter tuning. Moreover, it handles particularly well the problem of limited availability of training samples, typically encountered in biophysical parameter estimation applications.