The best and reliable method is to correlate the suspected clay layer data with lithology near the geophysical data. If you are using electrical resistivity method, for instance, resistivity of clay layer will be very low.
the determination of the clay layer depend upon its thickness, depth and the water salinity, if it is saturated with saline or fresh water as well as the environment of deposition. Generally, the resistivity, IP, TEM, and GPR are the best methods in determining the clay layer.
I recommend using TDIP (Time-domain induced polarization) which is so powerful for detecting the clay in the coastal area under high salinization circumstance. this related to my focus on my master thesis in mapping the clay along the Nile delta coast. It gives me amazing results in the coastal area which have a lot of challenges. So, I highly recommend using this tool in other environmental conditions.
I prefer to combine both induced polarization, and electrical resistivity methods , where , clays can show high values of charge ability and low values of resistivity.
There are few methods to identify the clay zones. First of all whether your target is in a shallow zone or a deeper zone. Secondly the availability of different instruments with you. I think TDIP (Time Domain Induced Polarization) is the most preferred technique to identify the clay zones. But it also can be investigated with the help of GPR (Ground Penetrating Radar) as well as terraTEM (using Time Domain / Transient Electro-magnetic technique). Combination of the borehole data with any of the above technique will help you to achieve the goal with high precession. If at all you don't have the bore hole data then also you can carry out the work with one of the above method.
I've used terraTEM in my master project in Andaman Coast and got very good results.