Multispectral and hyperspectral sensor data of the bio-optical parameters with a high spatial resolution are important for monitoring and mapping of the coastal ecosystems and estuarine areas, such as the Kneiss Islands in the Gulf of Gabes. Sentinel 2 S2A and Hyperion Earth observing-1 (EO1) imaging sensors reflectance data have been used for water quality determination and mapping of turbidity TU and chlorophyll Chl-a in shallow waters. First, we applied a tidal swing area mask based on uncorrelated pixel via 2D scatter plot between 665 nm and 865 nm to eliminate the overestimation of the concentration of water quality parameters due to the effect of the bottom reflection. The processing for mapping and validating Chl-a, Turbidity S2A, and EO1 were performed using a relation between reflectance bands and in situ measurements. Therefore, we were able to validate the performance of the case 2 regional coast colour processor (C2RCC) as well as our region-adapted empirical optical remote sensing algorithms. Turbidity was mapped based on the reflectance of 550 nm band for EO1 (R² = 0.63) and 665 nm band for S2A (R² = 0.70). Chlorophyll was mapped based on (457/528 nm) reflectance ratio (R² = 0.57) for EO1 and (705/665 nm) reflectance ratio (R² = 0.72) for the S2A.