This is the second part of a two-part paper developing and validating a structural model to describe the high rate anaerobic digestion of complex wastewater. A full-scale, two-stage hybrid upflow anaerobic reactor treating pig slaughterhouse effluent is assessed. Parameters and hydraulics are proposed for this system and validated. Characterisation of the system indicated that influent was a combination of equal parts (in terms of GOD) particulate fat, particulate protein, and soluble protein. Reactor hy draulics were close to completely stirred tank reactor (CSTR) hydraulics, as indicated by a residence time distribution (RTD) study. The Monday morning abattoir start-up was identified as a key disturbance suitable for parameter estimation. A stepwise parameter estimation procedure was used as proposed in the previous paper. An experimental data set without recycle was used for parameter estimation. The model with these parameters performed well on independent data sets with and without recycle. The model identified several anomalies in the experimental data that may be unique to reactors treating complex wastewater.