We present a novel design for a compact flow-through fluorescence detector for flow analyses applications and prove its functionality in the experiment. The detector operates by detecting the diffusely emitted fluorescence in a glass capillary, which is a measure for the concentration of the analyte to be detected. The fluorescence is excited via an axially coupled fibre providing LED light and is collected by a photodiode. As model analyte we used dissolved reactive phosphate. The determination of the phosphate concentration is based on the reaction of molybdate to phosphomolybdate, which quenches the fluorescence of Rhodamine 6G. The experiments rely on a reversed flow injection analysis system especially designed for decoupling the analytical setup from environmental pressure for in situ applications. By combining the optics part and the fluidic setup a measuring range of 0 - 40 μg L-1 PO4-P with detection limits of 0.22 μg L-1 PO4-P (7 nmol L-1) for water and of 0.45 μg L-1 PO4-P (14.5 nmol L-1) for seawater have been obtained. Our novel system has a sampling frequency of up to 300 samples per hour and achieves a repeatability between 0.6 % (RSD) for the blank value signal (n = 15) and 4.6 % (RSD) for a phosphate concentration of 20.8 μg L-1 PO4-P (n = 15).