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The shipboard measurements of optical and hydrological properties of seawater were used for development of regional bio-optical algorithms of waters of Peter the Great Bay. The shipboard measurements of chlorophyll-a and dissolved organic matter (DOM) concentrations were obtained by flow-through laser fluorometer (LF-3) (Institute for Automation and Control Processes, Vladivostok, Russia) and Sea-Bird Profiling CTD SBE-19plus (Conductivity, Temperature and Depth Sea-Bird Electronics, Sea-Bird Electronics, Inc., Washington, USA) equipped with WetStar fluorometers (WET Labs, Oregon, USA). The measurements were optically weighted according to light attenuation by depth. Ocean colour Moderate Resolution Imaging Spectroradiometer (MODIS)-Aqua data were used for our comparative analysis. Chlorophyll-a concentrations from ocean colour data were retrieved by OC3M, Garver-Siegel-Maritorena (GSM) and Carder algorithms. Relationships of the shipboard and satellite sensor data were analysed comparatively in our work. The Carder model gives the most general results of estimation of chlorophyll-a concentrations for all observed water cases. OC3M and GSM algorithms show good performance in case I water but they have large errors in the Amur Bay waters because of a large impact of the Razdolnaya river and Vladivostok city anthropogenic activity. Two regional chlorophyll-a algorithms were offered and they improve significantly the accuracy of chlorophyll-a concentration estimation. The first one is based on empirical regression between chlorophyll-a concentration and remotely sensed reflectance ratio. The second one uses satellite-derived values of sun-induced chlorophyll-a fluorescence when chlorophyll-a concentrations are higher than 3 mg m-3. The last one gives the best results for all water cases and provides an approach for separation between DOM produced by phytoplankton and DOM not connected with phytoplankton activity. This allows a regional DOM algorithm to be made. [ABSTRACT FROM AUTHOR]