Hi nnoufysalam,
I can give some general tips for your purpose. Of course there are so many details to handle via forum.
Regarding to the concentration boundaries of river water or sea water, you need to know first the groundwater flow direction. Do you have issues of seawater intrusion? If so, it is good to prescribe a fixed concentration on these nodes. If you have outflow from the model to the river boundary all the time, concentration may not be necessarily prescribed, just leave that FEFLOW computes these values. But if you want to simulate the interaction between river and aquifer, then concentration should be prescribed in case of inflow from river to aquifer.
FEFLOW provides possibility to use the so-called constraints in order to activate or deactivate boundary conditions. I guess you can find additional info in the forum and for sure in user manual and help system.
For the case of the artificial pond, you can prescribe both water levels and concentration as Dirichlet boundary condition, if these are known.
Percolation flux from the artificial pond can be easily computed using budget panels. There is a plenty of information about this in FEFLOW User Manual and Help System.
Hope you get some idea how to start...
Cheers,
Carlos