Self-Organizing Maps (SOM) have been used for patterning and visualizing ten environmental parameters and phytoplankton biomass in a mactrotidal (>10 m) Gyeonggi Bay and artificial Shihwa Lake during 1986–2004. SOM segregated study areas into four groups and ten subgroups. Two strikingly alternative states are frequently observed: the first is a diverse non-eutrophic state designated by three groups (SOM 1–3), and the second is a eutrophic state (SOM 4: Shihwa Lake and Upper Gyeonggi Bay; summer season) characterized by enhanced nutrients (3 mg l−1 dissolved inorganic nitrogen, 0.1 mg l−1 PO4) that act as a signal and response to that signal as algal blooms (24 µg chlorophyll-a l−1). Bloom potential in response to nitrification is affiliated with high temperature (r = 0.26), low salinity (r = −0.40) and suspended solids (r = –0.27). Moreover, strong stratification in the Shihwa Lake has accelerated harmful algal blooms and hypoxia. The non-eutrophic states (SOM 1–3) are characterized by macro-tidal estuaries exhibiting a tolerance to pollution with nitrogen-containing nutrients and retarding any tendency toward stratification. SOM 1 (winter) is more distinct from SOM 4 due to higher suspended solids (>50 mg l−1) caused by resuspension that induces light limitation and low chlorophyll-a (<5 µg l−1). In addition, eutrophication-induced shifts in phytoplankton communities are noticed during all the seasons in Gyeonggi Bay. Overall, SOM showed high performance for visualization and abstraction of ecological data and could serve as an efficient ecological map that can specify blooming regions and provide a comprehensive view on the eutrophication process in a macrotidal estuary.