This study analyzed the distribution, diversity, and density variation of algal clusters in a freshwater reservoir from an oceanic island and a traditional inland water system to gain insights on future marine freshwater resource management. In the Paldang water system (Han River), despite the upstream Paldang Dam and the downstream Jamsil underwater reservoir being in the same meteorological zone, their algae density patterns varied inversely. The distinct algal cluster structure (diversity/dominance) of Paldang was altered in the downstream reservoir, suggesting that physical devices aid algae management in traditional water systems. In contrast, 24 out of 35 genera (63.2%) identified in the Jeolgol Reservoir (Baeknyeong Island) were unique, lacking regulatory mechanisms, and existing in a complex ecotone. The desmid Chlorophyceae Cosmarium, adapted to higher photosynthetic stress and low temperatures, dominated in January (38.04%) and August (86.45%) during the periods of extreme photosynthetic stress. Jeolgol's annual algal cluster structure (H' 2.097; D 0.259; S' 35) demonstrated higher stability than Paldang (H' 1.125; D 0.448; S' 13) and the Jamsil underwater reservoir (H' 1.078; D 0.469; S' 12), maintaining an H' above 1.5 even during midwinters. No evidence of TN/TP inflow from surrounding soils was observed, even during torrential rainfalls, with phosphorus being the limiting factor for algal growth. TOC, BOD, chlorophyll-a, and turbidity peaked during Cosmarium bloom. Future climate change is expected to cause fluctuations in algal clusters and related water quality factors. The complex transitional nature of the Jeolgol Reservoir, its algal diversity, and the interspecies interactions contribute to the high stability of its algal community.