The Red Sea supports a diverse array of macrophyte species, including mangroves and seagrasses. Our study quantified the concentrations of 22 common elements, including trace metals, in mangrove and seagrass leaves and sediments to investigate the current pollution level in the Saudi Arabian Red Sea blue carbon habitat. Mangrove leaves were found to contain higher mean concentrations of total organic carbon (TOC), total nitrogen (TN), strontium (Sr), and tin (Sn) than seagrass leaves, which contained lower levels of sodium (Na), magnesium (Mg), phosphorus (P), sulfur (S), potassium (K), calcium (Ca), chromium (Cr), nickel (Ni), zinc (Zn), arsenic (As), molybdenum (Mo), cadmium (Cd), antimony (Sb), and lead (Pb) (p < 0.05). Concentrations of 16 elements were significantly higher in mangrove sediments, whereas higher levels of S, Ca, and Sn were found in seagrass sediments (p < 0.05). A positive correlation was identified between P and Cd concentrations in both mangrove and seagrass leaves (R > 0.35, p < 0.05), with a negative correlation to latitude (R <  − 0.30). Certain leaves of Halophila decipiens (5.42 mg kg⁻¹) and Halophila ovalis (5.08 mg kg⁻¹) exhibited Cr concentrations exceeding known toxicity levels for plants. Cr (127 mg kg⁻¹), Ni (60.0 mg kg⁻¹), Cu (24.7 mg kg⁻¹), Zn (263 mg kg⁻¹), and Cd (1.50 mg kg⁻¹) concentrations in certain Avicennia marina, Enhalus acoroides, Halodule uninervis, and Thalassia hemprichii sediments exceeded the sediment quality guideline levels, revealing the exposure of both ecosystems to varying degrees of trace metal pollution. Our study underscored the criticality of including both ecosystems in assessments to accurately evaluate the impact of pollution on coastal environments.