The Ciénaga Grande de Santa Marta (CGSM), Colombia is possibly the wetland that has experienced the largest mangrove mortality on record due to modification of hydrologic connectivity and consequent hypersaline conditions. We used hydroclimatic, salinity and mangrove basal area data collected in five stations from 1993 to 2015 to study the relation between ongoing mangrove recovery, changes in salinity in the wetland and hydroclimatic changes in precipitation, potential evapotranspiration and freshwater inputs. We found that until 2015, the mangrove ecosystems in CGSM are in general terms in a path of recovery due to the combined effect of favorable hydroclimatic conditions and management operations to increase freshwater inputs into the wetland. We observed in three stations that the annual growth of mangrove basal area increased as pore water salinity decreased. Regarding surface water salinity, El Niño/Southern Oscillation explained most of the inter-annual variability in the wet season by regulating freshwater and in the dry season by regulating potential evaporation from the wetland. However, persistent channel reopening appeared to be the cause for the largest salinity decreases, whereas lack of persistent dredging slowed recovery in other areas. The monitoring of the mangrove-salinity-hydroclimate system must continue in order to increase its understanding and to avoid more recurring episodes of mangrove mortality.