You should be examining your kayak on a regular basis to determine if it has suffered any damage and how much damage has been done. In case of some serious damage you should get it repaired by a professional or otherwise you can cover up small scratches yourself.
You do not have to be worried about small or superficial scratches. They can be left untreated and fine. Or else, you can apply a coat of polish and this will make the superficial scratches disappear.
If you feel the scratches are deeper, you can apply a coat of polyester gelcoat paint. Make sure you choose the colour that matches your kayak colour and for this you can test the paint by applying it on a small part of the boat. Also, read instructions before applying the paint.
You can also make the scratches disappear by blowing hot air on them through your hair drier or hot fan. This technique will not leave a need for paint or anything else to repair scratches.
You can also use torch flame. Blow them on the scratches and it will make them disappear quickly. You will not need anything else to cover them up. However, this technique is only effective if the kayak is made of polyethylene.
Another method is to treat deeper scratches and grooves is heating of metal spoon on them and this will make them disappear. However, it will depend how often you check your boat for scratches and any other damage. Do not leave it for long to examine your boat because sometimes the damage can be serious and permanent. So make sure you regularly examine your kayak, at least after every trip.