For the first time, based on a landscape approach, the features of the spatial distribution of benthic vegetation, floristic composition, and qualitative and quantitative characteristics of the macrophyto-benthos of the regional natural monument “Coastal Aquatic Complex at Cape Sarych” (Southern Coast of Crimea, Sevastopol region) are shown. The study used materials from hydrobotanical and landscape surveys conducted in this area in the summer of 2021. A landscape map of the water area was compiled, and seven underwater landscapes were identified, featuring the key macrophyte species Ericaria crinita, Gongolaria barbata and Phyllophora crispa. For each landscape contour, the total macrophyte biomass (TMB) and the proportion of key macrophyto-benthic species were calculated. The comparative analysis showed that the landscape of the shallow zone (0.5–1 m) has the greatest variability in TMB values (2036.5 ± 264.6)–(8167.6 ± 465.7) g·m−2 raw mass and proportions of E. crinita, G. barbata (4–83%). The contribution of epiphytes does not exceed (3–21% TMB). Maximum values of TMB (6972.8 ± 371.2)–(10 673.3 ± 654.8) g·m−2 raw mass and high contribution of E. crinita, G. barbata (53–77%) were observed in the landscapes upper shoreface (1–5 m), where the highest proportion of epiphytic algae was also recorded (23–34%). The TMB in landscapes of the gently (5–15 m) dipping accumulation plain was characterized by relatively low values, which varied slightly (1312.7 ± 141.3)–(2463.0 ± 196.7) g·m−2 raw mass, with the contribution of P. crispa increasing sharply with depth (from 20 to 87%), whereas that of E. crinita and G. barbata significantly decreasing (from 66 to 2%); the proportion of epiphytic plants was 8–23%. It was established that the marine flora contained a significant number of algal species listed in Red Data Books, which confirms the conservation value of the studied aquatic area. However, species of macrophytes, indirectly indicating pollution of the protected water area, were found in the algoflora of the nature monument. In the coastal zone under recreational pressure, a mass development of green algae (Ulva rigida, Ulva intestinalis, Cladophora laetevirens) was observed, along with the highest proportion of polysaprobic and the maximum contribution of annual and summer macrophyte species inhabiting waters with an elevated organic content. The obtained results can be utilized for optimizing the conservation regime of the natural monument.