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Declining water quality in streams and rivers has been a serious problem since 1960’s. One way to assess water quality is biodiversity study on benthic invertebrates. Benthic invertebrates are animals that live on rivers and lake bottoms. Any substrate change or any toxic chemical deposited in the bed of stream will affect its abundance. Biodiversity was correlated with water quality of the stream. The study was conducted to determine the biodiversity of benthic macro invertebrates in Badiangon spring and correlate it with the water quality of the stream. Inventory of benthic invertebrate’s species in three sampling spots revealed a total of 255 individuals in the three kick nets or 86 per kick net in 1 m x 1m area below the cobble substrate. This includes 9 species of fly, 7 species of snails, 4 species of larvae and 1 species of crab and scuds. Stonefly species is the most diverse in the three sampling spots. The stream is inhabited by the different groups of flies which are indicators of healthy stream site. The Shannon- Weiner index ranges from below 1. 5 (very polluted water) to 4.0 (unpolluted water). The diversity value of benthos in the area is 2.707, falls on the average range but may possibly decline and affects water quality in the future. The total biotic water quality score is 62.82 that indicates a good water quality but slightly impacted area. Chemical analysis showed that pH value, total dissolved solids and total hardness are within the normal range, which means less chemical pollutants. While microbiological analysis, showed that there is fungi, bacteria and fecal contamination in Badiangon spring water. Human intervention and anthropogenic pressures are inevitable. Therefore, protection and conservation of stream water shall be implemented to maintain the good water quality of Badiangon spring.