This study reports results on the estimated magnitude of changes in P sorption isotherms in clayey mud sediments when performed using (1) freeze-dried instead of fresh sediment samples and (2) artificial sea water (ASW) instead of ambient near-bottom water. The sediments used differed in their P sorption. For the isotherms, sediments were equilibrated for 48 h in solutions of varying P concentration whereafter the amount of P sorbed or desorbed was determined. We adjusted the modified Freundlich equation to the isotherm data and assessed differences in the isotherms between the treatments by comparing equilibrium P concentrations and P buffering capacities determined from the isotherm equation. Freeze-drying decreased the P sorption in all investigated sediments, but the magnitude of the changes varied depending on the properties of the sediments. The effect was minor in the sediment abundant in P sorption sites and low in easily exchangeable P, while it was clearer in the sediments originally high in P or low in sorption surfaces. ASW and ambient water produced similar isotherms suggesting that ASW is a suitable equilibrium solution in P exchange experiments with muddy clay sediments. This study enlightens the processes occurring in freeze-drying. The results highlight that when examining the effects of dissimilar treatments or experimental conditions on the P exchange isotherms the magnitude and significance of the observed changes should be evaluated in a proper context considering the precision of the method.Article highlightsThe effects of freeze-drying on P sorption isotherms are minor in sediments abundant in unoccupied sorption surfaces.Artificial sea water is a suitable background matrix for the P exchange isotherms.The precision of the method should be considered when comparing the effects of differing isotherm treatments.