Mathematical modelling in environmental biotechnology has been a traditionally difficult resource to access for researchers and students without programming expertise. The great degree of flexibility required from model implementation platforms to be suitable for research applications restricts their use to programming expert users. More user friendly software packages however do not normally incorporate the necessary flexibility for most research applications. This work presents a methodology based on Excel and Matlab-Simulink for both flexible and accessible implementation of mathematical models by researchers with and without programming expertise. The models are almost fully defined in an Excel file in which the names and values of the state variables and parameters are easily created. This information is automatically processed in Matlab to create the model structure and almost immediate model simulation, after only a minimum Matlab code definition, is possible. The framework proposed also provides programming expert researchers with a highly flexible and modifiable platform on which to base more complex model implementations. The method takes advantage of structural generalities in most mathematical models of environmental bioprocesses while enabling the integration of advanced elements (e.g. heuristic functions, correlations). The methodology has already been successfully used in a number of research studies.