To achieve a comprehensive characterization and provide the first historical reconstruction of trace metal contamination in southeastern Florida, five surface sediment samples and one sediment core were collected from waterways near Deering Bay and Paradise Point, at their intersection with Biscayne Bay. These waterways have been influenced by rapid urban development and hydrological modifications in surrounding watersheds. Metal concentrations were determined using inductively coupled plasma triple quadrupole mass spectrometry (ICP-TQMS). All analyzed metals were below the Probable Effect Level (PEL) for coastal sediments. However, copper exceeded the Threshold Effect Level (TEL) from 35 cm depth to the surface, warranting further monitoring. A Pb210 age model estimated an age of 122 years at 45 cm depth. Trace metal concentrations increased after the late 1800s, corresponding to early urban development, agricultural expansion, and Everglades drainage. Enrichment Factor (EF) and Geoaccumulation Index (Igeo) calculations indicated moderate to very high enrichment for elements such as silver, zinc, copper, cadmium, mercury and arsenic. Principal Component Analysis confirmed the anthropogenic signature of these contributions. The Potential Ecological Risk Index (PERI) revealed considerable ecological risk particularly in recent decades. Post-1970s environmental regulations possibly contributed to a decline in copper, lead, mercury, and cobalt levels. However, arsenic, cadmium, selenium, and zinc showed gradual increases towards the present, necessitating ongoing attention. Overall, sediment quality at Paradise Point does not pose a concern for the adjacent Deering Bay and Biscayne Bay waters, but continued monitoring is recommended to address emerging trends and ensure the long-term protection of these aquatic systems.