I chose to approach the Sian Ka'an Biosphere Reserve via the Muyil ruins. My initial plan was to visit the ruins and then walk the jungle boardwalk between the back of the ruins and the lagoon. That path is well marked on the OSM maps.
After a quick and easy drive from Tulum to Muyil, I arrived at the entrance of the Muyil ruins at 3.45pm only to discover they were closing at 4pm (November 2021). I went nevertheless. Arriving at the back of the ruins, I tried to explain to the guard at the back gate that my plan was to walk the jungle path to the lagoon and then walk back the dirt road to the parking. Without speaking Spanish, it was actually quite fun to explain and we both had some laughs. Unfortunately they were also closing the parking gate at 4pm, so that was not an option.
Therefore, change of plan, I took the car out of the ruins parking and started to drive the dirt road, next to the ruins, going to the lagoon. Half way there, there was a barrier and a guard. Waving at him, he just opened the barrier for me and showed me I could drive through. That allowed me to park at the lagoon. Retrospectively, it would have made more sense, in a biosphere reserve, to walk from the small parking to the lagoon.
So here I am, finally at the boardwalk start going through a kind of small gate. As I was alone all the way from the path start to the back of the ruins, I heard many noises of animals/birds moving or hiding when hearing my presence. But I didn't really get to see them. I also went to the top of the mirador (quite steep) to get a higher viewpoint on the reserve. There was a local there, probably waiting for some organized groups, but he didn't care about me. It was all very quiet as I was outside or between tours/groups hours.
Back to the lagoon, I saw some speedboats arriving full speed. That didn't motivate me to go through the lagoon by boat (previous reviews helped me in that choice as well). My freediving buddy that week did it through a tour, going by boat, walking the boardwalk and visiting the ruins. I'd rather do it my way. I haven't seen all of it (didn't swim), but I felt more in connection with nature being there alone.
Overall, I enjoyed my walk and visit. I didn't have to pay anything (except the entrance to the ruins of course); your mileage may vary. Somehow, I was wondering if they would close the path while I was there, or if I was allowed to do all this without paying extra. But that "worry" was quite useless. It was all fine, and I would not do it any other way. If I go back one day, I'll try that bumping "road" to Punta Allen.