Most of our CTD manuals refer to using downcast CTD data to characterize the profile. For typical configurations, downcast CTD data is preferable, because the CTD is oriented so that the intake is seeing new water before the rest of the package causes any mixing or has an effect on water temperature.
However, if you take water samples on the downcast, the pressure on an already closed bottle increases as you continue through the downcast; if there is a small leak, outside water is forced into the bottle, contaminating the sample with deeper water. Conversely, if you take water samples on the upcast, the pressure decreases on an already closed bottle as you bring the package up; any leaking results in water exiting the bottle, leaving the integrity of the sample intact. Therefore, standard practice is to monitor real-time downcast data to determine where to take water samples (locations with well-mixed water and/or with peaks in the parameters of interest), and then take water samples on upcast.