The restoration of mangroves has gained prominence in recent decades. Hydrological rehabilitation has been undertaken to connect impaired mangroves with the sea, lagoons or estuaries. Because mangrove hydrodynamics occurs on the surface and interstitial spaces in the sediment, we propose to determine the hydrological flow paths to restore the hydrological regimes of the impaired mangroves. The hydrological flow paths were determined through a micro basin analysis based on microtopographic data to generate a digital elevation model. Applying this methodological approach, the hydrology of an impaired area on a barrier island in the Gulf of Mexico was restored by excavating, desilting or clearing the channels on the identified hydrological flow paths. This area was compared to one in which impaired mangroves were reconnected to the marine lagoon but disregarding the flow paths. Data collected in both areas were evaluated by flood level analysis, using two methods: (i) a simple linear regression model (SLRM) and (ii) spectral analysis (SA), also known as dominant frequency analysis. The results suggest that restoration based on the hydrological flow paths was more effective than the direct opening to the nearest main water body without accounting for the microtopography. In both areas, soil salinity and sulfides decreased after hydrological reconnection. However, a greater efficiency in the investment of time and human resources was achieved when preferential flow paths were identified and taken into account. The methodological procedures described in this study are of universal application to other mangrove restoration programs.