Because the true state of complex physical systems is out of reach for real-world data assimilation problems, error covariances are uncertain and their specification remains very challenging. These error covariances are crucial ingredients for the proper use of data assimilation methods and for an effective quantification of the a posteriori errors of the state estimation. Therefore, the estimation of these covariances often involves at first a chosen specification of the matrices, followed by an adaptive tuning to correct their initial structure. In this paper, we propose a flexible combination of existing covariance tuning algorithms, including both online and offline procedures. These algorithms are applied in a specific order such that the required assumption of current tuning algorithms are fulfilled, at least partially, by the application of the ones at the previous steps. We use our procedure to tackle the problem of a multivariate and spatially-distributed hydrological model based on a precipitation-flow simulator with real industrial data. The efficiency of different algorithmic schemes is compared using real data with both quantitative and qualitative analysis. Numerical results show that these proposed algorithmic schemes improve significantly short-range flow forecast. Among the several tuning methods tested, recently developed CUTE and PUB algorithms are in the lead both in terms of history matching and forecast.