The pollution of the watercourses is one of the principal causes of the water emergency and, under the sanitary profile, one of the most complex and urgent problem within the Environmental Hygiene. The European Water Framework Directive 2000/60, has confirmed that for a correct qualitative evaluation of the superficial waters the monitoring must be inspired to the prevention and not only to the improvement. In our work we have experimented a new methodological approach to read and to understand the river ecosystem. The River Tronto and the River Tenna has been studied under the chemical-bacteriological profile and under the biological profile, through the Extended Biotic Index. The river continuum has been studied through the Functional Fluvial Index. The data have been correlated among through Principal Component Analysis. The statistic analysis underlines a direct correlation among the two biological indexes and a strong indirect correlation among these last ones and those of chemical-bacteriological nature. The pollution of the watercourses is one of the principal causes of the water emergency and, under the sanitary profile, one of the most complex and urgent problem within the Environmental hygiene. The European Water Framework Directive 2000/60, has confirmed that for a correct qualitative evaluation of the superficial waters the monitoring must be inspires to the prevention and not only to the improvement. In our job we have experimented a new methodological approach to read and to interpret the river ecosystem. The River Tronto and the River Tenna has been studied under the chemical-bacteriological profile and under the biological profile, through the Extended Biotic Index. The river continuum has been studied through the Functional Fluvial Index. The data have been correlated through Principal Component Analysis. The statistic analysis underlines a direct correlation among the two biological indexes and a strong indirect correlation among these last ones and those of chemical-bacteriological nature.