Classical habitat studies typically rely on a suite of unverified assumptions as follows: i) Treating habitat use as a direct indicator of its suitability assumes that all individuals can access the habitat equally. ii) Existing habitat models predict future spatial distribution of species based on static environmental factors, ignoring the dynamic nature of the environment. iii) Based on evolutionary theory, most habitat studies assume that animals use habitat in a manner to maximise their fitness. We hypothesised that the abovementioned assumptions are often incorrect, thus leading to false conclusions. By modelling habitat use of red deer, roe deer and wild boar in Slovenia we demonstrated the consequences of the misuse of these assumptions and provided guidance on how to avoid or mitigate them. The thesis is divided in three parts: i) We modeled red deer habitat using not only typical environmental factors as the explanatory variables, but also the cost distance (i.e. distance, reflecting habitat permeability) from the red deer reintroduction sites. The model predicted this variable as highly significant, showing that present red deer spatial distribution is not only reflected by the habitat suitability, but also by incomplete spatial spread of red deer. ii) We prepared a static predictive habitat model of wild boar, based on current values of temperature and precipitation, and three dynamic models taking into account different scenarios of temperature and precipitation changes by the year 2040. Incorporating climate change scenarios affected model predictions significantly: all three dynamic models predicted larger distribution range as well as increased local densities of wild boar, compared to the static model. iii) We compared the effects of chosen environmental factors on local population densities and individual fitness of red deer, roe deer and wild boar, respectively. In red deer, both supplemental feeding sites and spruce pole stands have significant positive influence on population density and negative influence on individual fitness. This indicates that red deer habitat use is irrational in terms of maximising fitness. According to our findings this is primarily related to habitat saturation, which in turn is tightly connected to anthropogenic land changes.