In this study two questions concerning the structure and organisation of shallow brackish and estuarine fish assemblages are: (1) Does the species number decline with lower salinity as found for the macrofauna invertebrates? (2) Does the water temperature during the year influence the abundance of fishes along the Swedish coast?In a west coast estuary salinities were higher but fluctuated more than in the Bothnian Sea. Days with temperatures exceeding 15°C were up to twice as many in the west coast estuary as in the Bothnian Sea. In spring the species number increased, but later on in summer it declined to increase again in autumn, but declined once again as winter approached. Fish density in the west coast estuary increased gradually to a maximum in late summer and then declined, while in the Bothnian Sea there was often a decline during summer. Positive correlations were found between observed minimum salinities and average species number, and between number of days with temperatures exceeding +15°C and both yearly average and maximum fish densities. Juveniles (0+) were present for longer periods in the west coast estuary than in the Bothnian Sea and reproduction of the common species started earlier in the former area. In winter the shallow areas are devoid of fish because of ice and so are re‐colonised each spring. The study demonstrates that water salinity limited the species number, and water temperature the abundance of fish.