A novel fluorimetric sensor for highly sensitive nitrite detection on the site is presented in this study. The proposed on-chip approach comprises the use of integrated polymer photodetectors to detect light from fluorescence reactions with a diaminofluorescein probe. The detectors were prepared with a heterostructured nanofilm of polythieno[3,4-b]thiophene/benzodithiophene and (6,6)-phenyl-C71-butyric-acid methyl-ester as a photoactive layer. Prior to fluorimetric detection, the quality of the spin-coated photoactive layer was characterized via nano-morphology and current-density measurements. Nitrite assays were conducted on a poly(methyl methacrylate) microchannel chip, to which polythienothiophene-C71 based detectors were aligned. Results of signal-to-noise ratio determination have indicated a detection limit below 0.55 μM, lower than the 0.1 mg L-1 maximum limit of operation in recirculating aquaculture systems for farming Atlantic salmon Salmo salar. An increase of the nitrite concentration to toxic levels may therefore be possible to detect. The fluorimetric sensor exhibited good linearity over three orders of magnitude and acceptable detection reproducibility, which confirmed its analytical value. Further tests revealed great promise of the integrated biosensor device for detecting nitrite in aquaculture-relevant samples with high precision. The approach reported hereby may provide impetus to in situ analytical tools for monitoring water quality at aquaculture facilities, the food industries or water monitoring stations.