I agree with "KAM". With the fill is only 2m deep, perhaps a couple of test pits would be able to check about the water above the clay. If you observe carefully, you may be able to see if water came down from the upper fill layer as you excavate (don't let the operator does the excavation and inspect later). I don't know how large an area is this, or how was the level of the in-situ clay before you add fill on top. By digging a few of test pits, you may find clues if water happens everywhere, or just at some pockets in area where the clay is lower than at other places. Pockets of water may indicate that it comes from the top, not from the bottom.
Is the area built up already ? It may be difficult to dig test pits, if the area has been developed. Another sleuthing work would be to drill a hole and collect the water sample. Also drill another hole, preferable in area where there is no fill, and deeper. Get another water sample. Hope that the second sample is groundwater. If chemical analyses of both samples are similar, likely, the water comes from below. If different, it is from surface. May be simple pH, electrical conductivity , chloride test, etc can do the job.
Thirdly, find out a little history and record for the period between the construction of the fill and now :
- settlement which occurs over time (indicate slow consolidation of clay.... 2m fill is not much additional load and unlikely to cause large settlement if the clay is stiff or hard)
- rainfall information... recent rainfall occurs?
- groundwater record of the area... is it common that water table may go up and ponding the ground surface (because of seasonal rising water table ?)
Lastly.... there may be an expensive way to trace water from the surface (rather than do chemical test). I worked on a dam which leaks, and we put some environmentally friendly dye upstream of the potential leakage area, and trace the colour further downstream of the dam.
Is it important that there is supposed to be no water above the clay ? Is the water kept building up with time ? Is settlement becoming a problem ? Perhaps your solution to use french drain is the most practical way !.
Hope this helps