The Pilon river sub basin is the conjunction for two physiographic provinces: Llanura Costera and Sierra Madre. Due to this, it posses topographic and physic variations that allow the development of twelve vegetation types, even endemism. These function on water absorption, sustains inhabitants livelihood, and a varied wildlife. Nevertheless, several processes related to population growth and agricultural expansions are causing the disappearance and fragmentation of this vegetation. During the period 1974 - 2000 at the coastal plains the torn scrub lost 86%, the mesquite scrub 73%, and the sub mountain scrub 32% whilst at the Sierra Madre sub mountain scrub lost 73 %, oak forest 43 % and fir forest 35%. Besides, there is a marked process of fragmentation which affects mainly to the Oak forest, the mixed forests of pine and oak, and the sub mountain scrub. In order to avoid that these processes alter water absorption and the agricultural production, a strategy for the adequate management of the natural resources of this sub basin was designed to conciliate the production needs with those of natural resources preservation. This identified three major lines of action: fragment preservation, conservative agriculture, and restoration. It also shows the optimal sites to develop these recommendable actions through spatial analysis carried on a geographic information system (GIS), using the method for river basin land allocation.