El curso alto del río Mataraña constituye un ejemplo representativo de los ríos de montaña mediterránea calcárea. El régimen hidrológico es pluvial mediterráneo, permanente, y conserva sus características naturales.
El curso del río discurre en buena parte de su recorrido por valles encajados, y hoces y desfiladeros propios del modelado kárstico. El lecho está constituido en algunos tramos por la roca madre, mientras que en otros predominan los sedimentos de granulometría media (gravas) que en ocasiones forman barras laterales de considerable espesor. El cauce presenta una amplia variedad de estructuras longitudinales, con presencia de combinaciones salto-poza, rápido-poza, y rápido-remanso, así como rápidos continuos y gradas.
Esta variedad de morfologías son el hábitat potencial de muchas especies indicadoras del buen estado y de la calidad de las masas de agua como es el caso de los odonatos inventariados (Calopteryx haemorrhoidalis, Onychogomphus sp.).
La continuidad y desarrollo de la vegetación riparia está limitada por las condiciones geomorfológicas destacando la mimbrera calcófila mediterránea que, a medida que descendemos en altitud, va mermando su alto grado de naturalidad inicial debido a la presencia de cañas (Arundo donax).
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