This article describes a small, autonomous low-cost system for real time monitoring in freshwater mesocosms. The instrument is able to measure temperature, infrared (IR) scattering, fluorescence induced by blue and ultraviolet (UV) light emitting diodes (LEDs) and the sunlight reflection. The device is based on measuring the fluorescence of the chlorophyll-a (chl-a) using an UV or blue LED. We tested the accuracy of the apparatus in a laboratory using serial dilutions of phytoplankton samples and we obtained a signal proportional to the chl-a concentration. Measurements were then performed in two mesocosms that had been maintained at different temperatures during the last decade, with one of them at ambient temperature, and the other 4°C warmer, in line with Intergovernmental Panel on Climate Change (IPCC) predictions. We found that the device described here was able to measure changes in chl-a concentrations of over 1.14μg/l and is capable of detecting CDOM (colored dissolved organic matter) which interfered in the fluorescence measurement. Moreover the designed system has a broad dynamic range, suitable for these kind of environments.