According to a few oral traditions from San Cristóbal Verapaz, the lake would have formed catastrophically by ground collapse during an earthquake in the early 16th Century, soon after the arrival of the Dominican friars (around 1525 CE), engulfing a church and its surrounding Maya settlement.

[2] This tradition is echoed in a book published in 1648 CE by the Irish Dominican friar Thomas Gage: "The English-American, or a New Survey of the West Indies".

However, an independent report by Spanish Dominicans also mentions the sudden formation of a lake near San Cristóbal, by cave collapse, during an earthquake in 1590 CE.

Most of the water therefore only restrict its circulation to the epilimnion, with an average residence time of 18 ± 3 days, assuming a constant mean depth of the termocline of 7 m (23 ft).

[6] The lake is fed by several streams, most noticeably by the Paná River in the west, which is born from the junction of Chijuljá and Requenzal creeks.

Other streams (Los Lavaderos, Chicojgual, Cerro Caj Coj) contribute very little to the lake water budget.

Lake Chichoj drains to Río El Desagüe, a tributary of the Cahabón River, which it joins after sinking into a cave for several hundreds of meters.

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[7] supports these testimonies.

[15] Contamination of the lake environment by chromium started in the 1950s, and has increased dramatically until at least 2005, reaching 20 times natural background levels.

[6] It originates in industrial activities that involve leather tanning in the shoe factory of Calzado Cobán.

[6] Most of the water hyacinth biomass is actually extracted from the lake to fight eutrophication and turned into horticultural fertilizer.

Demographic growth and lack of employment are some of the factors that have promoted conversion of forested areas into subsistence agriculture, especially following the coffee price crisis.

Various geologic data suggest that Lake Chichoj stretches above of a body of gypsum well exposed on outcrops farther west.

There, gypsum dissolution is responsible for repeated mountain flank collapses in the valley of Los Chorros.

In any case, it cannot be excluded that the lake level reverts in the future to its ancient stand, flooding areas that have now been filled and urbanized.