The Philippines is abundant in mineral resources, and mining can be considered a viable development option in pushing the country to trigger economic status. This study was conducted to determine the physico-chemical and microbial analysis of water of creeks within the Economic Mining Zone (EMZ), namely: Anahawan, Mahunok, Bulawanon, and Masabong creek in Sta. Cruz, Rosario, and Agusan del Sur, Philippines. Different parameters were selected; thus, a different method of analysis was being used, such as pH, Conductivity, Turbidity, Temperature, Salinity, Dissolved Oxygen, Biological Oxygen Demand, Total Dissolved Solids, mercury content, and bacteriological content. Total Mercury (ppb) samples were analyzed using a cold vapor technique, while for Biological Oxygen Demand and Dissolved Oxygen, Azide Modification Method was used. Other parameters, a 22 multi-parameter water quality, were used. The results showed that the physical parameters measured are within a tolerable limit or within the standard set by DENR. On the other hand, downstream of Bulawanon and Masabong Creek, mercury is traceable and above limit except for Mahunok Creek, wherein mercury level is below the detectable level. Moreover, the water analysis of all the sampled creeks are polluted with fecal coliform and failed from the standards set by Department of Environment and Natural Resources (DENR). It was recommended that miners or individuals present in the area should practice hygiene and provide good sanitary toilets not to enhance the presence of fecal coliform in the water to prevent other diseases. Also, there is a need to regularly monitor the Provincial Environment Office for water quality in the river to provide data for planning and monitoring the water’s current condition. There is also a need for massive information, education campaign for mining safety and hazards, and promote responsible mining by the Municipal and Provincial Environment Office in collaboration with the Mines and Geo-Science.