Abstract This paper addresses the QR decomposition and UD factorization based square-root algorithms of the recursive least-squares (RLS) Wiener fixed-point smoother and filter. In the RLS Wiener estimators, the Riccati-type difference equations for the auto-variance function of the filtering estimate are included. Hence, by the roundoff errors, in the case of the small value of the observation noise variance, under a single precision computation, the auto-variance function becomes asymmetric and the estimators tend to be numerically instable. From this viewpoint, in the proposed square-root RLS Wiener estimators, in each stage updating the estimates, the auto-variance function of the filtering estimate is expressed in a symmetric positive semi-definite matrix and the stability of the RLS Wiener estimators is improved. In addition, in the square-root RLS Wiener estimation algorithms, the variance function of the state prediction error is expressed as a symmetric positive semi-definite matrix in terms of the UD factorization method.