The majority of floristic and phytosociological studies conducted in the Atlantic Forest are focused on tree species and tree species communities, while only limited research is done on understory species, in particular concerning their interrelationship with environmental factors or their ecological requirements in terms of habitat change due to anthropogenic influences, such as complete and selective logging. In our study, the species abundance and vigor of three representative species of the Atlantic Forest in south-eastern Brazil (Gesneriaceae: Nematanthus crassifolius, Besleria melancholica; Acanthaceae: Stenostephanus lobeliaeformis) were measured in a riverine ecosystem that included different levels of past logging activities along environmental gradients such as altitude, exposure, inclination, and canopy openness. We measured the vigor of the species by counting the total number of shoots and estimating the rate of live shoots. To provide a comprehensive overview we developed a vigor index based on this data which might be useful for future studies on the response to environmental gradients of understory species in the tropics. The results show distinct relationships between various environmental factors and both species distribution patterns and vigor of the investigated species. N. crassifolius is strongly dependant on proximity to watercourses and open canopy conditions. Abundance of S. lobeliaeformis was limited to higher elevations, but according to our data individuals of this species are more vigorous at lower elevations of its distributional range. While being more vigorous with decreasing elevation, S. lobeliaeformis was completely absent at the lower end of the elevation gradient. The abrupt absence of this species at low elevations coincides with a complete forest clearance in the 1940s. S. lobeliaeformis was only found in the selectively logged forest. In contrast, changes in abiotic conditions have little effect on B. melancholica. We conclude that small-scale elevational and microclimatic gradients have differing consequences for the selected understory species. Those natural gradients are disturbed by a land-use gradient, and a scenario like this is typical of the Atlantic Rainforest at this elevation. Therefore a further understanding, especially of the largely undersampled understory plant community, is essential and a first approach in this direction is provided by this study.