The article is devoted to the issue of organization and possible improvement of the system of monitoring the state of marine and estuarine water areas and their changes due to anthropogenic activity on the example of the Tyligul estuary, the application of methods for reducing the level of eutrophication of the reservoir by installing artificial reefs. One of the main tasks in conducting ecological monitoring of marine coastal ecosystems, along with the assessment and forecast of their state, is the bioremediation of disturbed biocenoses. This applies primarily to biotic communities susceptible to the influence of the anthropogenic factor. Benthic communities are especially in need of ecological reconstruction in order to optimize the development process and their stability, as they are the most vulnerable to pollution of coastal waters.