[1] Lake Sentani lies at the foot of the Mesozoic mafic and ultramafic rocks of the Cyclops ophiolite mountains in a fault-controlled depression at an elevation of 73 metres (240 ft) above sea level.

[2] Lake Sentani is thermally stable, with temperatures ranging from 29 to 32 °C (84 to 90 °F) in the top 10 metres (33 ft); the surface pH is 6.2–6.8, and plankton levels are low at 1–2 mg/L except in the westernmost basin, where water circulation is limited, turbidity is doubled, and seasonal algal blooms, with resultant fish mortality.

[3][5][4] Preliminary bottom sediment samples from the eastern part of the lake have yielded sparse populations of arcellacean microfauna, dominated by Centropyxid types.

[8][9] Many of the Sentani people, who inhabit the islands, perimeter and environs of the lake, still have a traditional subsistence economy based on fishing and sago harvesting.

Many of the residents occupy dwellings built on posts over the lake, which thus serves as a depository for sewage, leading to locally high coliform bacteria counts,[10][11] but also to nutrient enrichment.

Recently a major reforestation project of grassland on the slopes surrounding the lake has been initiated, with the support of forest companies operating in Papua.

A major sustainable development issues for the inhabitants of the lake and surroundings is the existing proposal to build a hydroelectric power plant through a dam placed on the Jafuri river.