The round ponds/lakes in northern Siberia have a curious feature: they are very shallow with a flat bed. Explosions coming up out of the earth create craters like you would see if an artillery shell penetrated into the earth and exploded. These Siberian craters are flat and shallow therefore explosions of methane cannot be the cause.Such water-filled "bomb craters" could also come from natural methane gas explosions. Near the earth's surface there is methane which reacts explosively with oxygen when escaping. Since methane is unstable in air, it reacts quickly with oxygen to form CO2 and water. The freshly formed water then fills the crater.
I had once the assumption that the so-called volcano-mare in the Eifel of Germany could have originated in such a way. It is also not untypical that there are many such craters in Russia, because there is a lot of trapped methane.