Eutrophication can occur naturally, during the late stage of the natural ecological succession that accompanies the infilling of a lake. It then develops slowly, over thousands of years. It develops within only a few decades when triggered by cropland fertilization, industrial contamination, or urban development. Deforestation, land fertilization, urbanization and industrialization in the catchment of lake Chichoj are all thought to have contributed in a way or the other to the massive  lake contamination and eutrophication of the lake that has taken place since the 1950s. Degradation of its ecosystem motivated environmental studies starting in the 1970s. They aimed at documenting the eutrophication process, and at identifying its causes. Most concluded that the main source of eutrophication is the absence of treatment of  city waste waters, rather than agriculture.
The most visible consequence of eutrophication is the massive development of large floating rafts of the water hyacinth  (Eichhornia crassipes), which is untiringly harvested to prevent complete invasion of the lake open waters. The enormous amount of hyacinth removed from the lake is then composted to produce a horticultural fertilizer.
Many local witnesses have reported that the extensive marshes that surround the lake were open waters in the 1950s. The presence of a well marked shoreline 1.0 ± 0.1 to 1.4 ± 0.1 m above the average current lake level and surrounding the marshes supports these testimonies. Because eutrophication leads to rapid infilling of lakes by plant debris, and conversion of open waters to marshland, it has been hypothesized that eutrophication is responsible for the reduction in the lake surface.
Due to its location halfway between the Atlantic and Pacific Ocean, the lake ecosystem is normally influenced by the Pacific El Niño Oscillation (ENSO) and the North Atlantic Oscillation. Studies are under way to determine the sensitivity of the lake hydrology to these oscillations over the past millennium.