I presume the lagoon system you saw was the Laguna Nichupte'. If so, be aware that it's a protected reserve and the only way you can legitimately fish it is with a guide. That's not to say you couldn't do it on your own...I've seen it done there many times. The bridge areas by the Canal Nichupte' and Canal Nizuc are often fished at night for Tarpon by locals and tourists in the know.
For shorebound anglers fishing Mexican coastal waters (in non protected areas)..."no fishing license is required".
I've fished the Mayan Coast south of Cancun extensively and the Do-it-yourself opportunities are vast and productive. Further searches of flyfishing and travel boards should bring you rafts of information.