Based on the experience of managing coastal marine, and limans ecosystems of Ukraine, the theoretical scheme of Integrative Ecological Management is considered. The scheme includes the “Basic Diagnostic” block for which the key tools are: Basin Assessment, Ecosystem Approach and Ecosystem Services. Geo-information Technologies are demonstrated in order to assess the catchment areas of some limans and coastal marine ecosystems of Ukraine. With the ecosystem approach, it is necessary to use functional indicators for assessing autotrophic, heterotrophic and decomposer communities of the ecosystem, the bind of which is associated with Ecological Status of the water body. It is indicated that an important goal of environmental management is reducing the intensity of anthropogenic flows of substance and energy, which cause destruction of the ecological balance and devaluation of ecosystem services. For the second block of the scheme - “Decision Making” it is proposed to use Priority Management Algorithm principle as an effective tool which allows to achieve the target maximum at minimal cost. At the final stage of the “Target Result”, recommendations that are offered to stakeholders at the local, regional and national level must achievement the main objectives of the Integrative Ecological Management of coastal marine ecosystems and limans.

For the implementation of the Water Framework Directive and the Marine Strategy Framework Directive, numerous indicators based on macrophytes have been developed in coastal and shelf zones. However, transitional water bodies (e.g., estuaries, lagoons) have multiple overlaying strong environmental gradients that limit the assessment of the relationships between macrophyte ecological patterns and anthropogenic pressures. The aim of this study was to assess the abundance and distribution of macrophytes in the Curonian Lagoon and to analyze the spatial patterns of macrophyte species considering their morphofunctional properties (i.e., community surface index, which is the sum of the ratios between the specific surface of thallus structure elements and biomass of each macrophyte species in a sampling site) in relation to environmental factors, such as Secchi depth, salinity, wave exposure and area of wetlands. In the estuarine part of the Curonian Lagoon, the sampling of macrophytes was carried out in 2014–2015. Data on hydro-physical parameters were obtained from the water monitoring and hydrological model, while the CORINE data were used for the delineation of wetlands. The species diversity in the studied part of the Curonian Lagoon consisted 12 species (7 of them belong to phylum Chlorophyta and 5 to Magnoliophyta). From dominant algae, Chara contraria and Chara aspera mainly occurred along the northeastern part of the study area, whereas Cladophora glomerata mainly grew as epiphyte along the eastern shore of the lagoon. From dominant angiosperms, Potamogeton perfoliatus and Stuckenia pectinata occurred in the whole study area, while Myriophyllum spicatum rarely formed dense stands and usually was within the stands of charophytes or pondweeds. The salinity was the most important environmental factor, where the relative coverage of Zannichellia palustris, Potamogeton rutilus and all algae species, except Nitellopsis obtusa, correlated with salinity. The Secchi depth was of less importance and correlated with the relative coverage of N. obtusa, while a negative correlation was determined for S. pectinata. The mean community surface index depended on the depth gradient where it was significantly higher at ≤ 1.0 m depth than at 1.1–2.0 m depth. The community surface index significantly negatively correlated (the Spearman rS = −0.65) with the area of wetlands, which surrounded the eastern shore of the study area. Therefore, the tested morphofunctional index has a potential to define the ecological status considering macrophyte communities in the transitional water bodies.