The first thing you need to ask yourself before building a dynamic model is: what do I want to use this for? The answer to this question will give you an idea of what variables should be included, what things you can assume to be constant, what mechanisms need to be modelled, and what simplifying assumptions can be made.
There is currently a trend towards 'rigorous, first-principles, models'. The idea is that these models include all the possible mechanisms and are completely general purpose. This trend is completely stupid! No model is a perfect representation of reality - even the most complex model abstracts reality at some point (e.g. reaction kinetics, diffusion rates, etc). Including mechanisms and variables in a model that you don't really need doesn't make the model more 'accurate', but instead makes it much more complicated and difficult to maintain. The golden rule is to make models no more complicated than they have to be.
The basis of all dynamic models is the continuity equation. These equations may also include kinetic rate equations to model chemical reactions or transport rate equations to model heat or mass transfer. Models involving gas phases will often include thermo-dynamic equations of state. In some cases, equilibrium relationships can be used to simplify the model.