The Neotropical otter is a predator located in the upper trophic level; its geographical distribution stretches from northern Mexico to central Argentina. It lives in river banks, where it rests, plays, marks its territory, cleans its fur and breeds its offspring. Lontra longicaudis is sensitive to alterations in the habitat, either by the degradation of river bank environments and by pollution of water bodies; hence, it is considered as an indicator of the degradation of aquatic ecosystems. This species is currently included in the threatened species category according to NOM-059-SEMARNAT-2010. The aim of this work is to characterize the habitat and determine the abundance of the Neotropical otter in the upper part of San Diego River, to assess whether the sea otter population abundance is directly related on the characteristics of the habitat and the seasonal dynamics. The monitoring was carried out over two years (2012-2013). Eight kilometers along the river were sampled considering 3 segments of equal length, since preliminary visits revealed that these had distinctive physical and environmental characteristics. The physicochemical parameters of water were measured, plant species growing along the river bank were identified, 266 samples of feces were collected, and otter relative abundance was estimated. Segment 1 showed an acid water pH, with low temperatures and plant species of the genera Pinus, Quercus and Juniperus along the river banks; the second segment showed a neutral pH, with higher temperatures, and scarce riparian vegetation; the third segment again displayed riparian vegetation, with warm water and near-neutral pH. The relative abundance determined for the otter population averaged 0.46 otters/km. A model for predicting otter abundance was obtained, which yielded a prediction error of ± 0.27 otters/km. The characteristics of the habitat associated with otters in this area were similar to those described by other authors for other parts of the country, namely a neutral pH, clean oxygen-rich waters, low water temperature in the upper portions of the river, presence of riparian vegetation, with stretches of rapids and shallow areas with pools of slow-flowing, deep water. Separately, the abundance of otters found in this case lied within a range that differed from the one reported by other authors, which varies between 0.21 and 1.22 otters/km; again, this was not a fixed value, but varied over the sampling period: it decreased in the rainy season and rose in the dry season. The abundance-habitat relationship model showed an acceptable fit; however, the most significant variables were total dissolved solids, pH, flow zone and depth. This study made possible to determine the current status of the otter and the conditions of its habitat in this area; however, further studies are needed to gain a detailed understanding on the species to support decision-making and implement conservation actions.