In this paper a parameter estimation algorithm is developed to estimate uncertain parameters in two dimensional shallow water flow models. Since in practice the open boundary conditions of these models are usually not known accurately, the uncertainty of these boundary conditions has to be taken into account to prevent that boundary errors are interpreted by the estimation procedure as parameter fluctuations. Therefore the open boundary conditions are embedded into a stochastic environment and a constant gain extended Kalman filter is employed to identify the state of the system. Defining a error functional that measures the differences between the filtered state of the system and the measurements, a quasi Newton method is employed to determine the minimum of this functional. To reduce the computational burden, the gradient of the criterium that is required using the quasi Newton method is determined by solving the adjoint system.