La cabecera del río Pelagallinas es un ejemplo representativo de los ríos de montaña mediterránea silícea. La reserva está integrada por el cauce del arroyo de las Majadillas y el del arroyo Pelagallinas. El régimen hidrológico es pluvio-nival, permanente, sin alteración.
El curso del río, modelado sobre cuarcitas y pizarras, presenta un valle confinado en algunos tramos y un valle más amplio con una llanura de inundación estrecha y discontinua en otros. Tiene un trazado mayoritariamente sinuoso y meandriforme, a veces divagante. El caudal aumenta conforme avanza aguas abajo, pasando de ser un riachuelo a un río de cierta entidad a partir de su confluencia con el barranco de la Peña del Cuervo, que es un río caudaloso y totalmente natural, encajándose a partir de este punto en un cañón de gran pendiente.
La vegetación ribereña está representada por una aliseda hercínica y una sauceda negra continental. En las zonas altas el pinar de Pinus sylvestris ocupa las orillas junto con zarzales y espinares.
Destacan por su singularidad la zona de turberas de la parte alta por tratarse de un hábitat escaso en climas áridos, que presenta una alta biodiversidad y por lo tanto un alto valor ecológico.
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