The valley you walk through to get to Ciudad Perdida is laced by the Rio Buritaca, a fairly mighty river in places and one you will have to cross numerous times to reach your destination. In fact, on the third day of the trek you must ford it nine times! It can be quite deep in the wet season, up to the waist in cases but we were lucky to have it never above our knees due to the time of season and it being a particularly dry one at that. Still, having water sandals of some kind is advisable. Those that did not have them were definitely slowed down by having to stop and change repeatedly and many started walking through the river with their hiking boots on. This is fine for the river crossing but then you have wet shoes for the hike and for camp. Of course, that night was the coldest one of the trek and we were very happy to have our boots completely dry, and warm.
I suppose I should mention the kidnapping incident, although the chances of it happening again are very low. On September 10, 2003 Edwin Rey and another guide named Manuel were with a group of tourists at Ciudad Perdida when they were captured by a group of ELN rebels. Edwin and the other guide were tied up and left there, while eight of the tourists were taken away. There were initially thirteen tourists in the group, but the guerrillas decided not to take some of them for various reasons (one was sick with diarrhea, and two Australians were wearing sandals instead of hiking boots and were also rather 'gordo' according to Edwin, so the rebels didn't think they could handle the slog through the jungle). Eventually all eight hostages were released unharmed over the course of the next three months. It was a political kidnapping which was unsuccessful for the rebels, so it is unlikely they would attempt something like this again. Despite the media hype, it is actually very rare for foreigners to be kidnapped in Colombia (for wealthy/powerful Colombians it's a different story).
Now I've been in lots of places that are popular with mosquitoes, but Ciudad Perdida has to be the worst I have ever experienced. Along the trail is not too bad, but on the night you spend at the ruins be prepared to be eaten alive. Mosquito nets are provided in the sleeping area, but you can't stay under the net all the time, and plenty of them seemed to find their way into my net during the night anyway. Bring lots of repellant and clothes that are too thick for mosquitoes to bite through. Itineraries can vary and some groups spend two nights at the ruins, but I would strongly discourage this if only because of the mosquitoes.
On the way to the ruins you will have to cross back and forth across the river several times. The guides will be there to help you across, but be carefull as the currents can be very strong. Some people choose to cross barefoot or with flipflops, but I found it much easier to keep my shoes on, as the stones on the bottom can be very hard on bare feet and flipflops are easily lost in the current.