Multipath remains the main source of error when using lobal navigation satellite systems (GNSS) in constrained environment, leading to biased measurements and thus to inaccurate estimated positions. This paper formulates the GNSS navigation problem as the resolution of an overdetermined system, which depends nonlinearly on the receiver position and linearly on the clock bias and drift, and possible biases affecting GNSS measurements. The extended Kalman filter is used to linearize the navigation problem whereas sparse estimation is considered to estimate multipath biases. We assume that only a part of the satellites are affected by multipath, i.e., that the unknown bias vector is sparse in the sense that several of its components are equal to zero. The natural way of enforcing sparsity is to introduce an l1 regularization associated with the bias vector. This leads to a least absolute shrinkage and selection operator (LASSO) problem that is solved using a reweighted-l1 algorithm. The weighting matrix of this algorithm is designed carefully as functions of the satellite carrier to noise density ratio and the satellite elevations. The smooth variations of multipath biases versus time are enforced using a regularization based on total variation. An experiment conducted on real data allows the performance of the proposed method to be appreciated.