Substantial evidence shows that the frequency of hydrological extremes has been changing and is likely to continue to change in the near future. Non-stationary models for flood frequency analyses are one method of accounting for these changes in estimating design values. The objective of the present study is to compare four models in terms of goodness of fit, their uncertainties, the parameter estimation methods and the implications for estimating flood quantiles. Stationary and non-stationary models using the GEV distribution were considered, with parameters dependent on time and on annual precipitation. Furthermore, in order to study the influence of the parameter estimation approach on the results, the maximum likelihood (MLE) and Bayesian Monte Carlo Markov chain (MCMC) methods were compared. The methods were tested for two gauging stations in Slovenia that exhibit significantly increasing trends in annual maximum (AM) discharge series. The comparison of the models suggests that the stationary model tends to underestimate flood quantiles relative to the non-stationary models in recent years. The model with annual precipitation as a covariate exhibits the best goodness-of-fit performance. For a 10% increase in annual precipitation, the 10-year flood increases by 8%. Use of the model for design purposes requires scenarios of future annual precipitation. It is argued that these may be obtained more reliably than scenarios of extreme event precipitation which makes the proposed model more practically useful than alternative models.