A highly sensitive and simple analytical method is applied to the determination of Cs in estuarine and coastal waters. This analytical method combines adsorption of Cs on ammonium 12-molybdophosphate (AMP) and an ion exchange resin column, followed by subsequent ICPMS measurement. Significantly, the method requires a relatively small amount of sample volume (minimum volume: 20 mL) for the analysis by the selection of AMP with a low Cs impurity (0.02 ng-Cs mg⁻¹-AMP). The method has a detection limit of 1.0 ng L⁻¹ and a limit of quantification of 3.3 ng L⁻¹ based on replicate analyses of purified water samples. A sample storage strategy is also investigated: no time dependent changes are found in the concentrations for acidified samples (pH 1.0–1.5) used immediately (storage: 0 day) to those stored for two months in a dark place at room temperature (4–20 °C) or in a freezer (ca. −20 °C). Respective Cs concentrations of 95.8 ± 0.9, 202.8 ± 3.6 and 197.0 ± 1.9 ng L⁻¹ are obtained in estuarine water (SLEW-3), coastal seawater (CASS-4) and seawater (NASS-5) certified reference materials for heavy metals. In an application of the method to determination of Cs in estuarine and coastal regions of Japan, the obtained Cs concentrations vary from 11.2 to 306.4 ng L⁻¹ at a salinity range of 0.1 to 33.6.