Coastal waters are the richest parts of ocean ecosystems characterised by dynamic changes in water biology, physical and chemical features. Establishing local relationships between water constituents and optical properties in these areas will help to develop successful ocean colour algorithms allowing a thorough understanding of complex coastal waters and improving water quality monitoring. In this paper, the authors present the use of optical and biogeochemical measurements in complex aquatic environments and aim to create a semi-empirical model of remote-sensing reflectance (R_rs(λ_i)) for four wavelengths (λ_i = 420 nm, 488 nm, 555 nm, and 620 nm) based on multiparameter algorithms of absorption (a(λ_i)) and backscattering (b_b(λ_i)) coefficients. The bio-optical properties of water were determined based on empirical data gathered from aboard the r/v Oceania from April 2007 to March 2010 in chosen areas of the southern Baltic (Polish coast). The analyses reveal that R_rs(λ_i) in the studied area can be described with satisfactory accuracy using a five-parameter model. Positive results with a statistical error magnitude of R_rs(λ_i) of less than 50% were achieved for all four applied wavelengths. Bio-optical algorithms proposed by the authors enable evaluating biogeochemical characteristics of coastal areas in a broader context of ecosystem assessment and contribute significantly to the development of Earth and environmental sciences.