Funnily enough I was just noticing that mine looked nicely even yesterday lunchtime when I grabbed a quick lunch break.
The water runs off the roof into the rubber channel below the rear window - it has cut-outs just inboard of the boot lid each side and the water runs into the boot "moat" surround and to the rear where it goes under the black plastic trim strips - the drain pipes are located under there.
It should be relatively easy to remove the trim but you could always start by pushing a suitable tool such as a piece of cable up the drain tube from the bottom outlet first - that should dislodge any small bits of leaf and crud and you can pour water into the boot surround to flush it out.