EDIT: if you use the new MODFLOW-NWT, you probably don't need any of these because NWT does not use wetting-drying. So go for NWT if you can.
The biggest pain in the ass of groundwater modeling is getting your solution to converge.
This is the due to the uniqueness of groundwater system - the aquifers can be unconfined, in which case part of the aquifer is not fully saturated with water and the rest is saturated with water. In realty, the unsaturated part still has some residual water content and is called vadose zone. However, MODFLOW does not simulate water content in the vadose zone. It treats it as completely dry. This caused a huge problem when solving the model's linear system because cells has to be constantly switched between dry and wet to satisfy the boundary conditions. And this is often accompanied with abrupt changes making it even harder to converge. The 'rewetting' option can be turned off in the input file but that means once water level in a cell drop below the bottom in a solver iteration it will never come back. You may get a solution in the end but it will not be the correct solution.
Here are a couple of tricks/techniques to better assist you with model convergence.
1. First run it with rewetting on, if the residual fluctuates but the head change is small (around 1 m) then run it again using the previous solution as initial head with rewetting of this time. You should get a solution with good mass balance and correctly reflect the groundwater system you are trying to simulate.
2. If the above does not work, change all layer type to confined (laycon=0), then run the model. You should be able to obtain a solution with good mass balance easily. (If not, then there is something wrong with the model, check boundary conditions etc). Then using the solution as initial head, progressively change laycon of top layers to 3. For example, change layer 1 to type 3, run it, get a solution, use the new solution as initial head, change layer 1 and 2 to type 3...
