The current state of intertidal waters at Bottsand lagoon on the Baltic Sea coast, and on the mudflats off Schobüll on the North Sea coast of Schleswig-Holstein, Germany was assessed with a 36-month time series of water level, temperature, and salinity measurements. Periods of strong precipitation, high Elbe river discharge, and high solar radiation caused a higher data variability as compared to the off shore monitoring stations Boknis Eck in the Baltic and Sylt Roads in the North Sea.