Yes.
In Chetumal, water taxis use the main pier, "Muelle Fiscal", which is close to the big Government building, "Palacio Gobierno", at the waterfront at the south end of the main street through the centre of the city.
On my BelizeBus site, there is a map of Chetumal showing the locations of the ADO bus terminal and the pier. The pier is also visible on Google Earth.
http://belizebus.wordpress.com/