The present disclosure is directed to a method for estimating tower loads, such as tower deflection, of a wind turbine. The method includes receiving an estimate of slow variations in thrust of a tower of the wind turbine. The method also includes determining, via one or more sensors, tower accelerations of the tower of the wind turbine. Thus, the method also includes estimating the tower loads of the wind turbine as a function of the estimate of slow variations in thrust of the tower and the tower accelerations.