Benthic diatoms have been studied in different areas of the Mediterranean Sea, but no data have been available for Israeli coastal waters until the present time. In this work, the composition, ecology, and phytogeography of diatoms of the macrophytes epiphyton are presented for the first time. Altogether, 85 diatom taxa were found among the epiphyton of 25 species of green, brown, and red macroalgae from the Israeli coast between March and May of 2021. These diatoms represent three classes, 17 orders, 26 families, and 41 genera. The taxonomic composition, ecology, and phytogeography of species are discussed. The distribution of diatoms are compared to that of other macrophytes and anthropogenic loads across the shoreline. The dominant species are given. Ecological characteristics and abundance in communities of revealed species are represented and statistically analyzed. The index of saprobity S varies between 1.69–2.71. Sites that stressed aquatic communities are indicated. The influence of the anthropogenic loads on the coastal territories is defined as a major factor that stimulated diatom species richness. Sites with anthropogenic stress for aquatic communities are indicated. Based on the composition of bioindicators, it is concluded that the section of the Israeli coast studied is oligo-mesotrophic compared to the eutrophic Gulf of Tartus.