Possible physiological causes of the gradient in productivity in the area under study, established in Part I, are examined. Although total mineral uptake per unit area of vegetation is shown to be reduced from front to back of the fen, there is no correlation with any obvious limitation in the major nutrients, and no significant positional effect with added fertilizer. The main source of mineral supply is shown to be in the mud rather than in the water; and the hypothesis is advanced that increasingly anaerobic conditions in the mud, affecting the roots of Glyceria rather than Phragmites, may be the main factor responsible both for reduced total mineral uptake of the vegetation, and for the replacement of Glyceria by Phragmites at the back of the fen.