Semi enclosed waters, such as estuaries and lagoons, are vulnerable ecosystems that are experiencing persistent trace element (TE) contamination. Seagrasses have been reported worldwide as valuable bioindicator species for coastal contamination monitoring purpose. This is, to our knowledge, the first time the TE contamination of semi-enclosed ecosystems has been monitored along the full latitudinal gradient of the Moroccan Atlantic coast. In these ecosystems, the dominant seagrass species is Zostera noltei. 23 TEs (Fe, Al, Cr, Mn, Co, Ni, V, Cu, Zn, Sr, Li, As, Ag, Cd, Sn, Sb, Mo, Ba, Ti, Pb, U, Bi and Hg) and four major elements (Na, Mg, K, Ca) were measured in sediments and seagrass leaf samples were collected upstream and downstream of five semi-enclosed areas. They contrasted in both climatic conditions and levels of environmental contamination. The Trace Element Pollution Index (TEPI) and the Trace Element Spatial Variation Index (TESVI) were calculated from chemical element concentrations in the samples. Of the five semi-enclosed areas, Sidi Moussa lagoon’s sediments were the most contaminated (TEPI = 1.18). The TESVI differed highly between chemical elements among the five water bodies for sediments and seagrass leaves, the highest spatial variability being for Ag (TESVI = 72.01 and 21.05 respectively). For Z. noltei leaves, a latitudinal gradient of TE accumulation was recorded. A high bioconcentration factor (BCF > 1) for Cd, Mo, Sb, Ag, Zn and U indicated that the sediments were efficiently uptaken by the seagrass. Significant correlations (p < 0.05) between levels of Cd, Ag, Fe, Al, Ba, Hg, Mn and Zn in sediments and in Z. noltei leaves indicated similar contamination occurrences in both environmental matrices and their bioavailability for seagrasses. Overall, leaf TE bioconcentration among and within the study sites resulted from differences in element bioavailability and environmental conditions (climatic context, hydrological conditions and human impact). Ultimately, Z. noltei is a useful bioindicator of Cd, Mo, Sb, Ag, Zn, U, Al, Fe, Mn, Ba and Hg contamination in sediments.