Reliable monitoring of coastal waters is not possible without using remote sensing data. On the other hand, it is quite difficult to develop remote sensing algorithms that allow one to retrieve water characteristics (like chlorophyll-a concentration) in optically complex coastal and inland waters (called also Case II waters) as the concentrations of optically active substances (phytoplankton, suspended matter, and colored dissolved organic matter) vary independently from each other and the range of variability is often high. Another problem related to developing remote sensing algorithms for retrieving concentrations of optically active substances in such complex waters is vertical distribution of these substances. For example, phytoplankton distribution in the water column is often characterized with maxima just below the surface mixed layer, and some phytoplankton species even have the capability to migrate in the water column and tend to form layers at depths optimal for their growth. Twenty-three field campaigns were performed during the spring-summer period in the coastal waters of the southern Caspian Sea where vertical distribution of phytoplankton was measured by means of chlorophyll-a fluorometer. There results showed that there is usually a chlorophyll-a maximum between 10 and 20 m where the concentration is about one order of magnitude higher than in the top mixed layer. The Hydrolight 5.0 radiative transfer model used to estimate if the vertical distribution of biomass have detectable impact on remote sensing signal in these waters. For that purpose, several stations with distinctly different chlorophyll-a profiles were selected and two simulations for each of those measuring stations was carried out. First the Hydrolight was run with the actual chlorophyll-a vertical distribution profile and second a constant chlorophyll-a value (taken as an average of measured chlorophyll-a in the surface layer) was used in the model simulation. The modelling results show that the “deep” chlorophyll maximum has negligible effect on the remote sensing reflectance spectra. Consequently, there is no need to take into account the vertical distribution of phytoplankton while developing remote sensing algorithms for the Caspian Sea coastal waters.