Trace metal pollution has become an increasing concern in urban areas, mainly due to industrial activities and heightened human activities near water bodies. This study aimed to quantify the level of pollution caused by the trace metals Co, Cr, Cu, Mn, Ni, and Zn in surface sediments of Aurá and Guamá rivers, as well as Guajará Bay, in the metropolitan region of Belém (Northern Brazil). A total of 33 sediment samples were collected—14 from the Aurá River, 7 from the Guamá River, and 12 from Guajará Bay—during both the wet and dry seasons to capture seasonal variability. The studied trace metals were measured through inductively coupled plasma optical emission spectrometry (ICP-OES), and the decreasing order of concentration detected was the following: Mn > Zn > Cr > Ni > Co > Cu. To assess the degree of pollution, three geochemical indicators were employed: the Geoaccumulation Index (Igeo), which compares observed concentrations with natural background levels to classify contamination severity; the Enrichment Factor (EF), which helps distinguish between natural and anthropogenic sources of metals using a reference element (typically aluminum or iron); and the Mean-ERM-Quotient, which evaluates the potential ecotoxicological risk of the metals based on benchmark values for adverse effects on aquatic organisms. Based on these indicators, the sediments of the studied area can be classified as showing “moderate contamination and enrichment”. The metals Zn and Cu exhibited the highest degrees of enrichment, likely of anthropogenic origin. Overall, this study revealed that areas closer to sites of intense human activity are more susceptible to trace metal contamination, especially during the wet season. Frequent monitoring of areas classified as “contaminated” and time-series data are necessary to examine more deeply the pollution of river sediments and their potential changes concerning shifts in the status of urbanization and industrialization.