Management of forest production by application of Reduced Impact Logging (RIL) created crown opening by 13.3%, which was smaller compared with Conventional Logging (CNV) that caused crown opening by19.2%, and provided significant influence to water biodiversity. Availability of nutrient and essential minerals was better in RIL that was supported by high soluble residual or 95% higher and low velocity of river flow or 50% of surrounding CNV water. This physical condition showed significant difference to N and P ratio (N/P ratio) in RIL and CNV or 77.5 and 51.3. These values showed high content of nitrate of the water and it was in oligotropic type condition. Diversity Index of plankton in RIL was 1.754 and in CNV was 1.682 with each population density was 12,916 and 7,222 individuals/liter. The number of plankton had possitive correlation with N/P ratio (r = 0.9). In water catchment study area, there were found 28 fish species belonged to 20 genera and 8 families. The dominance families were Cyprinidae 57.14%, Bagridae 17.14%, and Anguillidae 7.14%. Most endemic fish species of Borneo were also found in both RIL and CNV water, however species with high relative frequency and density were found higher in RIL water.