I have a sit on top (sot) kayak (you can find pictures of my kayak here). I use this for fishing. One of drawback of this kayak is that it is easy to get wet: water comes in over wall. Because of its surfboard like design, this problem seems unavoidable. So, I have to wear properly to stay dry.
I checked some websites and books. Their recommendations are dry suit (expensive but sure), or bib style wader + rain jacket combo (less expensive but could-be deadly in case of falling). I think these options are over kill for freshwater kayak fisherman. Instead, I tested wader boots + bib style rain pants option, and it was fine for the purpose to keep myself dry. Of course, it was more comfortable to maneuver on kayak than other outfit options. I need test it under warm weather. So far, I am happy with this outfit option.