Estuarine environments are highly productive coastal ecosystems with a large intrinsic ecological value. Notwithstanding, they are often impacted by chemical contamination originating from several types of pollutants. Among these, trace metals are highly toxic, have an accumulative behaviour and can be transported for long ranges in suspended particles, representing a large environmental burden. This study aimed to assess the levels of contamination by the trace metals cadmium (Cd), cupper (Cu), iron (Fe), manganese (Mn), lead (Pb), and zinc (Zn) in the intertidal environments of the Óbidos Lagoon. The concentrations of metals were determined in water (dissolved and suspended fractions) and sediment samples, collected seasonally and over the course of 1 year in the intertidal water margins from four different sampling stations at the upper lagoon (Barrosa’s Branch: BB; Arnóia and Real rivers: AR; Covão dos Musaranhos: CM; Poça das Ferrarias: PF). In the water samples, Mn, Fe and Cd were the only metals observed in the dissolved fractions, while all the trace metals analysed were detected in the suspended fractions. The concentrations of the elements reflected the following patterns: Mn (0.077 ± 0.037 mg.L^-1) > Fe (0.026 ± 0.003 mg.L^-1) > Cd (0.026 ± 0.007μg.L^-1) for the dissolved fraction and Fe (14.553 ± 3.278 mg.L^-1) > Mn (1.116 ± 0.239 mg.L^-1) > Cu (0.028 ± 0.008 mg.L^-1) > Zn (0.021 ± 0.011 mg.L^-1) > Pb (3.060 ± 1.147 μg.L^-1) > Cd (0.073 ± 0.051 μg.L^-1) for the suspended fraction. The highest concentrations of metals in the water collum were observed at BB and AR stations during winter, highlighting the influence of precipitation and of the higher freshwater discharges from the main tributaries of the lagoon during this season. Sediments enriched with clay and with higher organic matter contents were prone to metal accumulation, presenting higher concentrations of all the analysed metals. Contamination by trace metals at the upper area of Óbidos Lagoon revealed to be of concern, and special caution as well as continuous monitoring should be encouraged for Cd and Pb.