Lake surface temperatures fluctuate between  in winter, and  in summer. From 1979 to 2011 annual rainfall was  at the lake, and  at Cerro La Laguna, the highest part of the catchment.  The residence time of water in the lake is therefore 35 ± 6 days assuming homogeneous water mixing. In actuality the lake is  strongly stratified and dimictic, being composed of a highly turbid and poorly mineralized epilimnion, over a 5 °C cooler, highly mineralized hypolimnion. 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 . The lake usually homogenizes in January or February, sometimes very rapidly.
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. Some springs feed the lake either directly near the shoreline (for example near Panconsul cave), or through the extensive marshlands that surround the lake. 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.  Some of the sewage of San Cristál Verapaz is rerouted away from the lake and flows in a pipe through the marshlands before being emptied into Río El Desagüe, downstream of lake Chichoj.
The lake results from the coalescence of at least three dolines, likely resulting from the dissolution of gypsum at depth. The occurrence of gypsum  is evidenced by a cluster of sulfate-bearing springs that dot the active trace of the Chixoy Polochic fault, 2 km south of the lake in the chixoy river valley, where they form large travertine fans.  Discharge at these springs is much larger than what their upslope catchments can provide. The catchment of Lake Chichój is the closest catchment susceptible to provide water to these springs, and it lies   above the springs.