The Caspian Sea hosts areas of high ecological value as well as industrial, leisure, and agricultural activities that dump into the water body different kinds of pollutants. In this complex context, a proper description of the origin and potential sources of pollution is necessary to address management and mitigation actions aimed at preserving the quality of the water resource and the integrity of the ecosystems. Here, we aimed at detecting sources of both nitrogen inputs, by N stable isotope analysis of macroalgae, and metals in macroalgae and sediments in two highly anthropized coastal stretches at the Iranian side of the Caspian Sea. Sampling was done near the mouth of rivers and canals draining agricultural and urbanized areas. In the westernmost waters, facing a port city, low macroalgal δ15N signatures indicated industrial fertilizers as the principal source of pollution. By contrast, in the central coastal waters, facing touristic areas, the high macroalgal δ15N indicated N inputs from wastewaters. Here the lowest dissolved oxygen concentrations in waters were associated with excess dissolved inorganic nitrogen. Metal concentrations varied largely in the study areas and were lower in macroalgae than in sediments. Localized peaks of Pb and Zn in sediments were observed in the central coastal sites as probable byproducts of mining activity transported downstream. By contrast, Cr and Ni concentrations were high in all sampling sites, thus potentially representing hazardous elements for marine biota. Overall, macroalgal δ15N coupled with metal analysis in macroalgae and sediments was useful for identifying the main sources of pollution in these highly anthropized coastal areas. This double approach in comprehensive monitoring programs could thus effectively inform stakeholders on major environmental threats, allowing targeted management measures.