In this thesis a bio-optical model was used in order to identify and characterise diversity and fertilisation effects on primary productivity in Freshwaters. The experiments were conducted in mesocosms, comprising 12 enclosures filled with water from two lakes with contrasting species diversity. Phosphorus was added to generate a three level phosphorus gradient. Vertical profiles of irradiance were combined with measurements of the spectrally averaged phytoplankton absorption coefficients and quantum yields of photosystem II in a bio-optical model and integrated over depth to obtain primary production estimates. Estimates derived from the bio-optical model were compared with results from 14C uptake experiments in order to evaluate the capacity of the bio-optical model to reflect photosynthetic processes and dynamics in freshwater phytoplankton communities.