One of the biggest problems with wastewater discharges is that its origin or root cause is currently unknown. This investigation tries to determine the root cause of the diffuse and punctual pollution of the water quality in Manzanillo Bay, located in Cristóbal, Colón district and province, of the Republic of Panama. A geographic analysis of basins and micro-basins was carried out to determine sources of the hydrological problem, based on mapping programs of the Digital Elevation Model (DEM) and the Shuttle Radar Topographic Mission (SRTM). In this study, the fall of bodies of water and the area with the greatest probability of generating discharges is verified, a central polygon was identified as the priority to analyze and it was inferred that within this unit is the polluting source of wastewater discharges, where it was determined that there is a punctual and not diffuse contamination. It is proposed to develop a tool to initiate ecological restoration that we want to be considered as a key element when establishing future pollution control networks. This study applies a methodology to address a current problem that covers two main issues of sustainable development: water and environmental sanitation. The research is a great starting step for the proper management of environmental sanitation in the study area.