For estimations of the ecological state of a lake and its future trends, data on seasonal and long-term variations of primary production are most necessary. The methods of in situ measurements of production are time consuming, rather complicated, and very expensive. Bio-optical model calculations provide a good alternative here. A semi-empirical model for estimating phytoplankton primary production (Arst et al., 2008, Aquatic Biology, Vol. 3, No. 1, pp. 19–30) allows calculating the vertical profiles and areal (integrated over water column) values of primary production using chlorophyll a concentration, incident irradiance, and light attenuation coefficient in the water. In the present study this model was developed further by elaborating its automated version. It enables performing rapid and greatly replicated estimations of the circumstantial variability of phytoplankton primary production at hourly intervals from morning to evening and as daily and monthly sums based on a table of initial parameters and depths. For demonstrating the practical application of the model we calculated primary production in two large eutrophic North-European lakes (Võrtsjärv and Peipsi), using a database collected during four warm months in 2009 (123 days in both lakes).
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