An automatic analyzer coupled with a versatile liquid waveguide capillary cell (LWCC) of different lengths for long-term in situ monitoring of nitrite in seawater was developed based on sequential injection analysis and spectrophotometry. Laboratory experiments have been carried out to analyze the impact of system parameters and environmental factors to obtain the optimal in situ detection performance of the analyzer. By utilizing 10 cm and 50 cm LWCCs, the analyzer can detect nitrite (NO2−) concentrations from 0.063 to 6.5 μM and 0.025 to 0.5 μM, and reach detection limits of 0.0189 μM and 0.0076 μM respectively. The short optical path (10 cm) analyzer was tested in situ during a scientific research cruise and then deployed at a coastal experiment station for one month to test the analyzer long-term measurement reliability and monitor nitrite temporal variation. The long optical path (50 cm) analyzer was deployed in a low nutrient coral reef waters over 50 days and the CTD, turbidity, dissolved oxygen and chlorophyll a data were synchronously acquired through a multi-parameter probe, and the distinct relationship between the in situ monitoring results was discussed. •An in situ analyzer with a versatile liquid waveguide capillary cell module was developed to detect nutrients in seawater.•By utilizing 50 cm LWCC, the analyzer can detect nitrite from 0.025 to 0.5 μM and reach a detection limit of 7.6 nM.•Two long-term in situ deployments were completed with the autonomous nitrite analyzers in different environments.