To gather information on the state of health of the two rivers, a monitoring index tool called the Benthic Index of Biological Integrity or B-IBI was adopted and modified from the index used by the Environmental Protection Agency (USA). The Index looks at assemblages of invertebrates to assess the scale of stress. Specifically, it uses four classes of biological attributes (metrics) that reflect responses of the river to gradients of human influence and these are: richness and composition of groups (taxa), taxa tolerance, feeding dynamics (ecology), population attributes. Rivers with B-IBI scores from 46-50 are considered in excellent condition while those with 10-16 are very poor.

Three sites from each river were selected. They represent the highest accessible point, mid-river, and mouth. For Lipadas those are Barangays Guianga, Alambre, and Sirawan. For Talomo, those are Barangays Tamayong, Angalan, and Talomo. Their B-IBI health ratings ranged from very poor to generally poor. In Lipadas River, Guianga Station was assessed to be generally poor, Alambre Station was seen to be commonly poor while
Sirawan Station was evaluated to be very poor. Meanwhile, in Talomo River, Tamayong Station was assessed to be generally poor, Angalan Station was evaluated to be poor to very poor and Talomo Station was very poor.

Stoneflies, which are highly intolerant to pollution, were never found in both rivers throughout the study. When stoneflies show up in future monitorings, which can be a sign that the river is getting cleaner.

The B-IBI annual health profile of the two rivers forms baseline information for succeeding monitoring activities on the health of these rivers. The comparatively poorer health in Talomo stations indicated that those areas were experiencing more stress than the fair to poor ratings in Lipadas. However, the mouths of both have deteriorated as exemplified by months when no organisms were collected. The four classes of biological attributes generally got low scores indicating that the chemical, physical, and biological environment of the two rivers have been altered.

To pretest a simple indicator protocol that could be easily learned and used by non-scientists, a simplified version of the B-IBI was jointly developed by the Biological Monitoring groups in Cebu and Davao. This is called the 2-metric Protocol that makes use of only two criteria, namely: dominance and tolerance. This was pretested in Brgys. Alambre and Tamayong. The results of the pretest revealed that while the simplified version can be easily tallied by a lay-volunteer, the ratings could be less rigorous than that of the B-IBI. In critical decisions, the B-IBI should be the point of reference.