Parameters of convective ventilation and also the content and composition of free amino acids and free carbohydrates in roots, basal culm internodes and leaves were investigated in five stands of Phragmites australis that were subjected to different growth conditions and salinity levels. Shoot length, stem diameter and productivity decreased with increasing salinity. These morphometric variations in turn affected parameters of convective ventilation and amino acid patterns. Phragmites populations growing at the highest salinity levels possessed the lowest rhizome conductivities, which was probably caused by their more pronounced xeromorphic growth. High counterpressures of the rhizome system and low stem diameters were limiting factors for convective flows. The Phragmites stand with lowest flow rate and ventilation efficiency had the highest percentage of alanine, serine and γ-aminobutyric acid (55% of total free amino acids) in its roots, indicating hypoxic stress in basal plant parts. Increasing salinity was connected with significantly higher fractions of glutamine (in basal culm internodes), glutamate (in roots) and proline (in both) as well as slightly increasing osmolality of plant sap. However, total contents of free amino acids and carbohydrates were low, and not related to either salinity level or osmolality of plant sap. This suggests that they might not have an important, direct role as an osmolyte in P. australis. Stand-specific variations in amino acid and carbohydrate patterns of leaves were negligible. Ratios of amino acids to carbohydrate were positively related to potential N supply. It is concluded that (1) salinity affects convective rhizome ventilation by varying the reed morphometry, and (2) the pattern of free amino acids responds characteristically to conditions of salinity and hypoxic growth.