The determination of nitrate nitrogen (NO3-N) in recirculating aquaculture systems is of great significance for the health assessment of the living environment of aquatic animals. Unfortunately, the commonly used spectrophotometric methods often yield unstable results, especially when the ambient temperature varies greatly in the field measurement. Here, we have developed a novel handheld absorbance measurement sensor based on the thymol-NO3-N chromogenic rearrangement reaction. In terms of hardware, the sensor adopts a dual channel/dual wavelength colorimeter structure that features a modulated light source transmitter and a synchronous detector receiver. The circuit measures the ratio of light absorbed by the sample and reference containers at two LEDs with peak wavelengths at 420 nm and 450 nm. Using the modulated source and synchronous detector rather than a constant (DC) source eliminates measurement errors due to ambient light and low frequency noise and provides higher accuracy. In terms of software, we design a new quantitative analysis algorithm for absorbance by studying colloid absorbing behavior. The application of a buffer operator embedded in the algorithm makes the sensor get the environmental correction function. The results have shown that the sensitivity, repeatability, precision and environmental stability are higher than that by ordinary spectrophotometry. Lastly, we have a brief overview of future work.