Algae reduce and methylate arsenate and the end product of the reaction is correlated to their growth rate. At slow growth rates, dimethylarsinate (DMA) is produced, and at fast growth rates arsenite (As(III)) is produced. Previous work has linked this phenomenon to the phosphorus luxury uptake mechanism of algae, and a model was developed for the process (Hellweger et al. Limnol. Oceanogr. 2003, 48, 2275). This paper presents the integration of that process model for arsenic transformation by algae into a full ecological model and application to Lake Biwa, Japan. The model application allows for a quantitative analysis of the field data, consistent with the process model and the ecological dynamics of the lake. The newly developed ecological model includes a variable phytoplankton composition, which is needed to simulate luxury uptake. This is in contrast to most existing ecological models, which typically assume a fixed "Redfield" composition. The model adequately reproduces the observed ecology of Lake Biwa, including the rapid uptake of phosphate by phytoplankton without immediate growth (luxury uptake) following lake overturn. The model also reproduces the observed arsenic speciation, including the gradual appearance of DMA during the summer and peaks in As(III) concentration at the onset of spring and fall algal blooms.