This work provides a preliminary study of the destination, mobility, and availability of tributyltin (TBT), dibutyltin (DBT), and monobutyltin (MBT) in contaminated sediments and water column within Puerto Rosales Port, located in the middle zone of the Bahía Blanca Estuary (Argentina). Therefore, this study presents the first comprehensive results of the role of several physicochemical parameters (temperature, pH, Eh, salinity, turbidity, organic matter, chlorophyll, and macronutrients) in behavior of organotin compounds (OTCs) in a marine-coastal ecosystem. The samples were collected seasonally in May, August, and November during 2014. Levels of OTCs were determined in sediments and water column samples by means of gas chromatography-mass spectrometry analysis. Degradation index analyses suggested not recent inputs of TBT at the area of study. However, results submitted a continuous input of TBT into the column water; further, its distribution and degradation pattern were shown to be influenced by salinity, turbidity, particulate organic matter, chlorophyll, and nitrates. These last two parameters, chlorophyll and nitrates, also were very important for sediment samples. Chlorophyll together with high temperatures recorded in the surface sediments triggers biodegradation process of TBT and DBT resulting in high MBT levels while nitrates seemed to promote debutylation process. Furthermore, pH appeared to influence drastically the adsorption/desorption activity of TBT and DBT in sediment. Finally, the Eh obtained suggested a degradation of TBT thanks to the presence of Fe (III) in this compartment. In addition, in fact, the results outlined a possible MBT additional input that contributes to the pollution observed in the study area. Graphical abstract Organotin compounds behavior according to several physicochemical parameters.