Although mathematical modelling of biological wastewater treatment processes has proved to be valuable for large-scale WVVTPs (wastewater treatment plants) little experience has been acquired in the mathematical modelling of small wastewater treatment plants. This paper seeks to evaluate the applicability of mathematical modelling on small systems, which are characterized by high fluctuations in organic and hydraulic loads and little possibility for control. In order to achieve this, the paper examines the different steps in a general modelling protocol. One important bottleneck for the general use of mathematical modelling of small systems that emerges is the frequent sampling and many analyses needed for characterization of the flows while its applicability is limited. On the other hand, the determination of the model structure of a small WWTP can be quite valuable. Experiments show that tracer tests should include tests with a highly varying influent flow rate to spot independent small internal flows as these can have a significant impact on the behaviour of peak concentrations throughout the system. In addition, the model structure determination can provide useful information on dead zones, short-circuiting and mixing behaviour in the plant.