The corrosion protection of metallic structures by modification of their surface by using new, environmentally and economically acceptable methods is one of the challenges of modern industry. The application of thin, well-ordered films of organic molecules has a great potential in metal surface modification by preventing the penetration of water and aggressive ions towards the surface. While organic acids, such as phosphonic and carboxylic, have become popular surface modifiers for metal oxides in various fields, especially in the past decade, there is still a lack of consensus on deposition protocols, especially on alloys, as well as on their stability under realistic application condition. The aim of this thesis is to find the most suitable method of forming well-defined and stable self-assembled layers of longchain phosphonic and carboxylic acids on the surface of AISI 316L stainless steel and cupronickel alloy providing good corrosion protection in natural waters. Three preparation methods were used for this purpose: dip-coating, spraying and electrochemical method. For each method the influence of parameters, such as drying and adsorption temperature, drying and adsorption time, applied potential, etc., was examined. Since the most important feature of the obtained films is corrosion protection, their fundamental characterization was conducted by two electrochemical techniques: polarization measurements and electrochemical impedance spectroscopy. Selected samples were additionally characterized by spectroscopic techniques (infrared and Raman spectroscopy), electron and optical microscopy and goniometry. Based on these results, for testing of stability of the protective films in realistic conditions, the method of spraying octadecylphosphonic acid was selected, due to easier film formation and very high corrosion resistance observed in simulated seawater. After defining the optimal conditions for the film formation, the durability of such corrosion protection was tested in flow conditions. Also, the protection against microbially influenced corrosion in natural waters was studied by electrochemical techniques and the surface analysis. These measurements have shown that octadecylphosphonic acid films provide good corrosion protection at all tested media flow rates on both tested alloys, thereby successfully reducing the possibility of microbiogically infuenced corrosion. The last step of the research was to investigate the possibility of in-situ repair of the protective film.