As far as earthquakes, tsunamis and other natural disasters are concerned, San Juan del Sur is pretty safe.
In San Juan del Sur, it is possible to have a tsunami. From memory, the last tsunami we had was 14 years ago, and it was a small one. Because of the topography and the form of the bay in San Juan del Sur, the mainland is protected from much of the roughness of the ocean. The way that everything is laid out, Costa Rica also protects San Juan del Sur from larger and damaging waves.
If you move more to the north of San Juan del Sur, there are fewer bays, so the land is more open to the sea, which increases the probability of a tsunami. From memory again, the last problem from a tsunami was more than 60 years ago.
Unless you buy something in the lowlands and essentially in a flood plain, you don’t have to worry about flooding in San Juan del Sur. In the entire area from Costa Rica past San Juan del Sur, you will find very few areas where flooding is any kind of a problem at all.
San Juan del Sur also doesn’t have significant earthquakes. The faults are mainly in other parts of Nicaragua, far enough away that when there is an earthquake in Managua, even though they feel it in San Juan del Sur, it will not be enough to cause damage. It’s pretty safe.
San Juan del Sur doesn’t have problems with brush fires like they have in places like California.
As far as hurricanes, most of the hurricanes come to Nicaragua from the Atlantic Ocean, and San Juan del Sur is on the Pacific side. San Juan del Sur is very well protected from hurricanes.