A method includes producing formation fluid from a subsurface in situ heat treatment process. The formation fluid is separated to produce a liquid stream and a gas stream. At least a portion of the liquid stream is provided to a hydrotreating unit. At least a portion of selected in situ heat treatment clogging compositions in the liquid stream are removed to produce a hydrotreated liquid stream by hydrotreating at least a portion of the liquid stream at conditions sufficient to remove the selected in situ heat treatment clogging compositions.