The assimilation of satellite-based water level observations (WLOs) into 2D hydrodynamic models can keep flood forecasts on track or be used for reanalysis to obtain improved assessments of previous flood footprints. In either case, satellites provide spatially dense observation fields, but with spatially correlated errors. To date, assimilation methods in flood forecasting either incorrectly neglect the spatial correlation in the observation errors or, in the best of cases, deal with it by thinning methods. These thinning methods result in a sparse set of observations whose error correlations are assumed to be negligible. Here, with a case study, we show that the assimilation diagnostics that make use of statistical averages of observation-minus-background and observation-minus-analysis residuals are useful to estimate error correlations in WLOs. The estimated correlations do not behave as expected; however, analysis shows that the diagnostic can also be used to highlight anomalous observation datasets. Accurate estimates of the observation error statistics can be used to support quality control protocols and provide insight into which observations it is most beneficial to assimilate. Furthermore, the understanding gained in this paper will contribute towards the correct assimilation of denser datasets.