Practical clean analytical methods for the monitoring of Ba, Mn, Cu and Ni in estuarine waters with salinity ranging from near zero to about 32‰ are reported. Three longitudinal surveys were conducted on the levels of Ba, Mn, Cu and Ni for Selangor River and Klang River from the upper estuary freshwater points to the river mouth. In addition, monitoring of dissolved Ba were carried out at a fixed estuarine station of the Selangor River over the daily flood-ebb tidal cycles for a neap tide and two spring tide occassions. The longitudinal surveys show both input and removal of the trace metals monitored during estuarine mixing. The fixed station study shows that the concentrations of dissolved Ba vary in the range from 3.4 to 5.7μg/L for neap tide samples, whereas concentrations ranging from 6 to 120μg/L were observed for spring tide samples. Variations of the trace metal concentrations over the daily tidal cycles and sample standing were dependent on the water salinity, pH, dissolved oxygen and suspended solids levels.