Pollution assessment was performed by using NO
3-, NO
2-, coprostanol (5β(H)-Cholestan-3β-ol), and cholestanol (5α(H)-Cholestan-3β-ol) at the 42 sampling points in the rivers in Shimabara and Unzen. NO
2- was detected at the 2 sampling points and exceeded 0.04 mg L
-1. NO
3-N + NO
2-N concentrations exceeded 10 mg L
-1 at the 18 sampling points. The highest concentration was 27.5 mg L
-1. High concentrations of NO
3-N were observed in the northern parts of the study area. Coprostanol concentrations at the 8 sampling points exceeded 700 ng L
-1 (Australian drinking water standard). Coprostanol has a potential to distinguish the nitrate pollution sources. The sterols ratio (5β/(5β+5α)) exceeded 0.5 at the 18 sampling points. It revealed that fecal pollution occurred.
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